DC-Build-Header: librostlab-blast 1.0.1-2 / Mon Jan 28 04:38:19 +0000 2013 DC-Task: logfile:/tmp/librostlab-blast_1.0.1-2_unstable_clang.log version:1.0.1-2 chroot:unstable modes:binary-only:clang source:librostlab-blast architecture:any esttime:268 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang librostlab-blast_1.0.1-2' Could not create '/sbuild-nonexistent/logs': No such file or directory Could not create '/sbuild-nonexistent/logs': No such file or directory sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-29-139-51.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ librostlab-blast 1.0.1-2 (amd64) 28 Jan 2013 04:38 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: librostlab-blast Version: 1.0.1-2 Source Version: 1.0.1-2 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/librostlab-blast-ifTosb/librostlab-blast-1.0.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/librostlab-blast-ifTosb' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-68619075-adfa-45e8-a180-0207d4e9da80' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [227 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Get:3 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:4 http://localhost unstable/main 2013-01-27-2011.16.pdiff [737 B] Get:5 http://localhost unstable/main 2013-01-27-2011.16.pdiff [737 B] Get:6 http://localhost unstable/main Sources [8236 kB] Get:7 http://localhost unstable/main amd64 Packages [8284 kB] Get:8 http://localhost unstable/main 2013-01-28-0212.01.pdiff [43 B] Get:9 http://localhost unstable/main 2013-01-28-0212.01.pdiff [43 B] Fetched 16.8 MB in 3s (4783 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'librostlab-blast' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/rostlab/librostlab-blast/trunk/ Need to get 390 kB of source archives. Get:1 http://localhost/debian/ unstable/main librostlab-blast 1.0.1-2 (dsc) [2380 B] Get:2 http://localhost/debian/ unstable/main librostlab-blast 1.0.1-2 (tar) [384 kB] Get:3 http://localhost/debian/ unstable/main librostlab-blast 1.0.1-2 (diff) [3691 B] Fetched 390 kB in 0s (1503 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + echo 'Add experimental as repository' Add experimental as repository + echo deb http://localhost:9999/debian experimental main + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Get:1 http://localhost experimental Release.gpg [836 B] Hit http://localhost unstable Release Get:2 http://localhost experimental Release [161 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Get:3 http://localhost experimental/main Translation-en [704 kB] Get:4 http://localhost experimental/main amd64 Packages [1605 kB] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Fetched 2471 kB in 1s (1333 kB/s) Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Hit http://localhost experimental Release.gpg Hit http://localhost unstable Release Hit http://localhost experimental Release Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Ign http://localhost experimental/main amd64 Packages/DiffIndex Get:1 http://localhost experimental/main Translation-en/DiffIndex [7819 B] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Hit http://localhost experimental/main amd64 Packages Fetched 7819 B in 1s (3932 B/s) Reading package lists... + apt-get install --yes --no-install-recommends clang -t experimental Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: clang-3.2 compiler-rt cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base gcc-4.8-base libc-dev-bin libc6 libc6-dev libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libgcc1 libgomp1 libitm1 libllvm3.2 libncurses5 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsqlite3-0 libssl1.0.0 libstdc++6 libstdc++6-4.7-dev libtinfo5 mime-support python python-minimal python2.7 python2.7-minimal Suggested packages: gcc-4.7-locales g++-4.7-multilib gcc-4.7-doc libstdc++6-4.7-dbg gcc-4.7-multilib libmudflap0-4.7-dev libgcc1-dbg libgomp1-dbg libitm1-dbg libquadmath0-dbg libmudflap0-dbg libcloog-ppl0 libppl-c2 libppl7 binutils-gold glibc-doc libstdc++6-4.7-doc python-doc python-tk python2.7-doc binfmt-support Recommended packages: llvm-3.2-dev manpages-dev file The following NEW packages will be installed: clang clang-3.2 compiler-rt gcc-4.8-base libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libllvm3.2 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support python python-minimal python2.7 python2.7-minimal The following packages will be upgraded: cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libitm1 libncurses5 libquadmath0 libstdc++6 libstdc++6-4.7-dev libtinfo5 15 upgraded, 21 newly installed, 0 to remove and 24 not upgraded. Need to get 56.7 MB of archives. After this operation, 72.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ experimental/main gcc-4.8-base amd64 4.8-20130127-1 [147 kB] Get:2 http://localhost/debian/ experimental/main libc6-dev amd64 2.16-0experimental1 [3086 kB] Get:3 http://localhost/debian/ experimental/main libc-dev-bin amd64 2.16-0experimental1 [226 kB] Get:4 http://localhost/debian/ experimental/main libc6 amd64 2.16-0experimental1 [4729 kB] Get:5 http://localhost/debian/ experimental/main libgcc1 amd64 1:4.8-20130127-1 [43.7 kB] Get:6 http://localhost/debian/ experimental/main libstdc++6 amd64 4.8-20130127-1 [335 kB] Get:7 http://localhost/debian/ experimental/main libtinfo5 amd64 5.9+20130119-1 [294 kB] Get:8 http://localhost/debian/ experimental/main libncurses5 amd64 5.9+20130119-1 [115 kB] Get:9 http://localhost/debian/ experimental/main libncursesw5 amd64 5.9+20130119-1 [142 kB] Get:10 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-4 [1213 kB] Get:11 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.15.2-1 [463 kB] Get:12 http://localhost/debian/ experimental/main libexpat1 amd64 2.1.0-2 [138 kB] Get:13 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:14 http://localhost/debian/ experimental/main libgomp1 amd64 4.8-20130127-1 [27.4 kB] Get:15 http://localhost/debian/ experimental/main libitm1 amd64 4.8-20130127-1 [37.7 kB] Get:16 http://localhost/debian/ unstable/main libllvm3.2 amd64 3.2-2 [7865 kB] Get:17 http://localhost/debian/ experimental/main libobjc4 amd64 4.8-20130127-1 [163 kB] Get:18 http://localhost/debian/ experimental/main libquadmath0 amd64 4.8-20130127-1 [139 kB] Get:19 http://localhost/debian/ experimental/main libstdc++6-4.7-dev amd64 4.7.2-19 [1678 kB] Get:20 http://localhost/debian/ experimental/main g++-4.7 amd64 4.7.2-19 [5877 kB] Get:21 http://localhost/debian/ experimental/main gcc-4.7 amd64 4.7.2-19 [5831 kB] Get:22 http://localhost/debian/ experimental/main cpp-4.7 amd64 4.7.2-19 [5416 kB] Get:23 http://localhost/debian/ experimental/main libgcc-4.7-dev amd64 4.7.2-19 [2465 kB] Get:24 http://localhost/debian/ experimental/main gcc-4.7-base amd64 4.7.2-19 [148 kB] Get:25 http://localhost/debian/ experimental/main mime-support all 3.53~experimental2 [36.5 kB] Get:26 http://localhost/debian/ experimental/main libpython2.7-minimal amd64 2.7.3-15 [531 kB] Get:27 http://localhost/debian/ experimental/main python2.7-minimal amd64 2.7.3-15 [1220 kB] Get:28 http://localhost/debian/ experimental/main libpython2.7-stdlib amd64 2.7.3-15 [2367 kB] Get:29 http://localhost/debian/ experimental/main python2.7 amd64 2.7.3-15 [326 kB] Get:30 http://localhost/debian/ experimental/main python-minimal amd64 2.7.3-10 [41.8 kB] Get:31 http://localhost/debian/ experimental/main python amd64 2.7.3-10 [184 kB] Get:32 http://localhost/debian/ experimental/main libobjc-4.7-dev amd64 4.7.2-19 [717 kB] Get:33 http://localhost/debian/ experimental/main libclang-common-dev amd64 3.2-1~exp5 [303 kB] Get:34 http://localhost/debian/ experimental/main compiler-rt amd64 3.2-1~exp5 [315 kB] Get:35 http://localhost/debian/ experimental/main clang-3.2 amd64 3.2-1~exp5 [10.1 MB] Get:36 http://localhost/debian/ experimental/main clang all 3.2-1~exp5 [9506 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.7 MB in 1s (34.1 MB/s) Selecting previously unselected package gcc-4.8-base:amd64. (Reading database ... 13484 files and directories currently installed.) Unpacking gcc-4.8-base:amd64 (from .../gcc-4.8-base_4.8-20130127-1_amd64.deb) ... Setting up gcc-4.8-base:amd64 (4.8-20130127-1) ... (Reading database ... 13491 files and directories currently installed.) Preparing to replace libc6-dev:amd64 2.13-38 (using .../libc6-dev_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc6-dev:amd64 ... Preparing to replace libc-dev-bin 2.13-38 (using .../libc-dev-bin_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6:amd64 2.13-38 (using .../libc6_2.16-0experimental1_amd64.deb) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Checking for services that may need to be restarted... Checking init scripts... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.16-0experimental1) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Checking for services that may need to be restarted... Checking init scripts... Nothing to restart. (Reading database ... 13509 files and directories currently installed.) Preparing to replace libgcc1:amd64 1:4.7.2-5 (using .../libgcc1_1%3a4.8-20130127-1_amd64.deb) ... Unpacking replacement libgcc1:amd64 ... Setting up libgcc1:amd64 (1:4.8-20130127-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libstdc++6:amd64 4.7.2-5 (using .../libstdc++6_4.8-20130127-1_amd64.deb) ... Unpacking replacement libstdc++6:amd64 ... Setting up libstdc++6:amd64 (4.8-20130127-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libtinfo5:amd64 5.9-10 (using .../libtinfo5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libtinfo5:amd64 ... Setting up libtinfo5:amd64 (5.9+20130119-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libncurses5:amd64 5.9-10 (using .../libncurses5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libncurses5:amd64 ... Setting up libncurses5:amd64 (5.9+20130119-1) ... Selecting previously unselected package libncursesw5:amd64. (Reading database ... 13509 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130119-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-4_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.15.2-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-2_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Preparing to replace libgomp1:amd64 4.7.2-5 (using .../libgomp1_4.8-20130127-1_amd64.deb) ... Unpacking replacement libgomp1:amd64 ... Preparing to replace libitm1:amd64 4.7.2-5 (using .../libitm1_4.8-20130127-1_amd64.deb) ... Unpacking replacement libitm1:amd64 ... Selecting previously unselected package libllvm3.2:amd64. Unpacking libllvm3.2:amd64 (from .../libllvm3.2_3.2-2_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8-20130127-1_amd64.deb) ... Preparing to replace libquadmath0:amd64 4.7.2-5 (using .../libquadmath0_4.8-20130127-1_amd64.deb) ... Unpacking replacement libquadmath0:amd64 ... Preparing to replace libstdc++6-4.7-dev 4.7.2-5 (using .../libstdc++6-4.7-dev_4.7.2-19_amd64.deb) ... Unpacking replacement libstdc++6-4.7-dev:amd64 ... Preparing to replace g++-4.7 4.7.2-5 (using .../g++-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement g++-4.7 ... Preparing to replace gcc-4.7 4.7.2-5 (using .../gcc-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.2-5 (using .../cpp-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement cpp-4.7 ... Selecting previously unselected package libgcc-4.7-dev:amd64. Unpacking libgcc-4.7-dev:amd64 (from .../libgcc-4.7-dev_4.7.2-19_amd64.deb) ... Preparing to replace gcc-4.7-base:amd64 4.7.2-5 (using .../gcc-4.7-base_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7-base:amd64 ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.53~experimental2_all.deb) ... Selecting previously unselected package libpython2.7-minimal:amd64. Unpacking libpython2.7-minimal:amd64 (from .../libpython2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Unpacking libpython2.7-stdlib:amd64 (from .../libpython2.7-stdlib_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-15_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3-10_amd64.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-10_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.2-19_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package compiler-rt. Unpacking compiler-rt (from .../compiler-rt_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang-3.2. Unpacking clang-3.2 (from .../clang-3.2_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../clang_3.2-1~exp5_all.deb) ... Setting up libc-dev-bin (2.16-0experimental1) ... Setting up libc6-dev:amd64 (2.16-0experimental1) ... Setting up libncursesw5:amd64 (5.9+20130119-1) ... Setting up libssl1.0.0:amd64 (1.0.1c-4) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Setting up libsqlite3-0:amd64 (3.7.15.2-1) ... Setting up libexpat1:amd64 (2.1.0-2) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libgomp1:amd64 (4.8-20130127-1) ... Setting up libitm1:amd64 (4.8-20130127-1) ... Setting up libllvm3.2:amd64 (3.2-2) ... Setting up libobjc4:amd64 (4.8-20130127-1) ... Setting up libquadmath0:amd64 (4.8-20130127-1) ... Setting up gcc-4.7-base:amd64 (4.7.2-19) ... Setting up libgcc-4.7-dev:amd64 (4.7.2-19) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.2-19) ... Setting up cpp-4.7 (4.7.2-19) ... Setting up gcc-4.7 (4.7.2-19) ... Setting up g++-4.7 (4.7.2-19) ... Setting up mime-support (3.53~experimental2) ... Setting up libpython2.7-minimal:amd64 (2.7.3-15) ... Setting up python2.7-minimal (2.7.3-15) ... Linking and byte-compiling packages for runtime python2.7... Setting up libpython2.7-stdlib:amd64 (2.7.3-15) ... Setting up python2.7 (2.7.3-15) ... Setting up python-minimal (2.7.3-10) ... Setting up python (2.7.3-10) ... Setting up libobjc-4.7-dev:amd64 (4.7.2-19) ... Setting up libclang-common-dev (3.2-1~exp5) ... Setting up compiler-rt (3.2-1~exp5) ... Setting up clang-3.2 (3.2-1~exp5) ... Setting up clang (3.2-1~exp5) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7' + cd /usr/bin + for VERSION in '$VERSIONS' + rm g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Ytduow/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/710 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14674 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev, bison, doxygen, flex, graphviz, latex-xcolor, librostlab-dev, texlive-fonts-recommended, texlive-latex-extra Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), autotools-dev, bison, doxygen, flex, graphviz, latex-xcolor, librostlab-dev, texlive-fonts-recommended, texlive-latex-extra dpkg-deb: building package `sbuild-build-depends-librostlab-blast-dummy' in `/«BUILDDIR»/resolver-983lHt/apt_archive/sbuild-build-depends-librostlab-blast-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install librostlab-blast build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bison bsdmainutils debhelper doxygen ed file flex fontconfig fontconfig-config gettext gettext-base graphviz groff-base html2text intltool-debian latex-xcolor libasprintf-dev libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libcairo2 libcdt4 libcgraph5 libcroco3 libcups2 libcupsimage2 libdatrie1 libdbus-1-3 libfontconfig1 libfreetype6 libgcrypt11 libgd2-noxpm libgettextpo-dev libgettextpo0 libglib2.0-0 libgnutls26 libgpg-error0 libgraph4 libgraphite3 libgs9 libgs9-common libgssapi-krb5-2 libgvc5 libgvpr1 libice6 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg8 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms1 liblcms2-2 libmagic1 libopenjpeg2 libp11-kit0 libpango1.0-0 libpaper-utils libpaper1 libpathplan4 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libpoppler19 libptexenc1 librostlab3 librostlab3-dev libsigsegv2 libsm6 libtasn1-3 libthai-data libthai0 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxft2 libxml2 libxmu6 libxpm4 libxrender1 libxt6 luatex m4 man-db po-debconf poppler-data preview-latex-style tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-dejavu-core ttf-marvosym x11-common xdg-utils Suggested packages: bison-doc wamerican wordlist whois vacation dh-make doxygen-doc doxygen-gui gettext-doc gsfonts graphviz-doc groff cups-common rng-tools libgd-tools krb5-doc krb5-user libjasper-runtime liblcms-utils liblcms2-utils ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp librostlab-doc less www-browser libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-unfonts-core perl-tk xpdf-reader pdf-viewer gv postscript-viewer libfile-which-perl dot2tex gvfs-bin Recommended packages: doxygen-latex curl wget lynx-cur autopoint ttf-liberation dbus libglib2.0-data shared-mime-info fonts-droid krb5-locales xml-core texlive-luatex libmail-sendmail-perl lmodern ruby wish texlive-fonts-recommended-doc tex-gyre tipa texlive-latex-base-doc texlive-latex-extra-doc texlive-latex-recommended-doc latex-beamer prosper texlive-pictures-doc pgf libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autotools-dev bison bsdmainutils debhelper doxygen ed file flex fontconfig fontconfig-config gettext gettext-base graphviz groff-base html2text intltool-debian latex-xcolor libasprintf-dev libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libcairo2 libcdt4 libcgraph5 libcroco3 libcups2 libcupsimage2 libdatrie1 libdbus-1-3 libfontconfig1 libfreetype6 libgcrypt11 libgd2-noxpm libgettextpo-dev libgettextpo0 libglib2.0-0 libgnutls26 libgpg-error0 libgraph4 libgraphite3 libgs9 libgs9-common libgssapi-krb5-2 libgvc5 libgvpr1 libice6 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg8 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms1 liblcms2-2 libmagic1 libopenjpeg2 libp11-kit0 libpango1.0-0 libpaper-utils libpaper1 libpathplan4 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libpoppler19 libptexenc1 librostlab3 librostlab3-dev libsigsegv2 libsm6 libtasn1-3 libthai-data libthai0 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxft2 libxml2 libxmu6 libxpm4 libxrender1 libxt6 luatex m4 man-db po-debconf poppler-data preview-latex-style sbuild-build-depends-librostlab-blast-dummy tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-dejavu-core ttf-marvosym x11-common xdg-utils 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 92.0 MB/92.0 MB of archives. After this operation, 270 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.2-1 [39.9 kB] Get:2 http://localhost/debian/ unstable/main groff-base amd64 1.22.1-2 [741 kB] Get:3 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.4 [210 kB] Get:4 http://localhost/debian/ unstable/main man-db amd64 2.6.3-3 [898 kB] Get:5 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-10 [27.2 kB] Get:6 http://localhost/debian/ unstable/main libgpg-error0 amd64 1.10-3.1 [77.9 kB] Get:7 http://localhost/debian/ unstable/main libgcrypt11 amd64 1.5.0-3 [298 kB] Get:8 http://localhost/debian/ unstable/main libp11-kit0 amd64 0.12-3 [52.8 kB] Get:9 http://localhost/debian/ unstable/main libtasn1-3 amd64 2.13-2 [67.7 kB] Get:10 http://localhost/debian/ unstable/main libgnutls26 amd64 2.12.20-3 [618 kB] Get:11 http://localhost/debian/ unstable/main libkeyutils1 amd64 1.5.5-4 [8690 B] Get:12 http://localhost/debian/ unstable/main libkrb5support0 amd64 1.10.1+dfsg-3 [49.2 kB] Get:13 http://localhost/debian/ unstable/main libk5crypto3 amd64 1.10.1+dfsg-3 [112 kB] Get:14 http://localhost/debian/ unstable/main libkrb5-3 amd64 1.10.1+dfsg-3 [394 kB] Get:15 http://localhost/debian/ unstable/main libgssapi-krb5-2 amd64 1.10.1+dfsg-3 [148 kB] Get:16 http://localhost/debian/ unstable/main libidn11 amd64 1.25-2 [178 kB] Get:17 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-2 [202 kB] Get:18 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.31-2 [247 kB] Get:19 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-7 [903 kB] Get:20 http://localhost/debian/ unstable/main libsigsegv2 amd64 2.9-4 [28.9 kB] Get:21 http://localhost/debian/ unstable/main m4 amd64 1.4.16-4 [260 kB] Get:22 http://localhost/debian/ unstable/main flex amd64 2.5.35-10.1 [332 kB] Get:23 http://localhost/debian/ unstable/main libavahi-common-data amd64 0.6.31-1 [134 kB] Get:24 http://localhost/debian/ unstable/main libavahi-common3 amd64 0.6.31-1 [54.3 kB] Get:25 http://localhost/debian/ unstable/main libdbus-1-3 amd64 1.6.8-1 [173 kB] Get:26 http://localhost/debian/ unstable/main libavahi-client3 amd64 0.6.31-1 [59.1 kB] Get:27 http://localhost/debian/ unstable/main libfreetype6 amd64 2.4.9-1.1 [451 kB] Get:28 http://localhost/debian/ unstable/main ttf-dejavu-core all 2.33-3 [1021 kB] Get:29 http://localhost/debian/ unstable/main fontconfig-config all 2.9.0-7.1 [233 kB] Get:30 http://localhost/debian/ unstable/main libfontconfig1 amd64 2.9.0-7.1 [300 kB] Get:31 http://localhost/debian/ unstable/main libpixman-1-0 amd64 0.26.0-3 [427 kB] Get:32 http://localhost/debian/ unstable/main libpng12-0 amd64 1.2.49-3 [190 kB] Get:33 http://localhost/debian/ unstable/main libxau6 amd64 1:1.0.7-1 [18.8 kB] Get:34 http://localhost/debian/ unstable/main libxdmcp6 amd64 1:1.1.1-1 [26.3 kB] Get:35 http://localhost/debian/ unstable/main libxcb1 amd64 1.8.1-2 [50.1 kB] Get:36 http://localhost/debian/ unstable/main libx11-data all 2:1.5.0-1 [189 kB] Get:37 http://localhost/debian/ unstable/main libx11-6 amd64 2:1.5.0-1 [901 kB] Get:38 http://localhost/debian/ unstable/main libxcb-render0 amd64 1.8.1-2 [18.5 kB] Get:39 http://localhost/debian/ unstable/main libxcb-shm0 amd64 1.8.1-2 [10.3 kB] Get:40 http://localhost/debian/ unstable/main libxrender1 amd64 1:0.9.7-1 [32.2 kB] Get:41 http://localhost/debian/ unstable/main libcairo2 amd64 1.12.2-2.1 [912 kB] Get:42 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.33.12+really2.32.4-5 [1838 kB] Get:43 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.6-2 [134 kB] Get:44 http://localhost/debian/ unstable/main libcups2 amd64 1.5.3-2.14 [255 kB] Get:45 http://localhost/debian/ unstable/main libjpeg8 amd64 8d-1 [134 kB] Get:46 http://localhost/debian/ unstable/main libjbig0 amd64 2.0-2 [32.2 kB] Get:47 http://localhost/debian/ unstable/main libtiff4 amd64 3.9.6-11 [202 kB] Get:48 http://localhost/debian/ unstable/main libcupsimage2 amd64 1.5.3-2.14 [137 kB] Get:49 http://localhost/debian/ unstable/main libdatrie1 amd64 0.2.5-3 [28.6 kB] Get:50 http://localhost/debian/ unstable/main libgd2-noxpm amd64 2.0.36~rc1~dfsg-6.1 [229 kB] Get:51 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:52 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-10 [145 kB] Get:53 http://localhost/debian/ unstable/main x11-common all 1:7.7+1 [278 kB] Get:54 http://localhost/debian/ unstable/main libice6 amd64 2:1.0.8-2 [63.1 kB] Get:55 http://localhost/debian/ unstable/main libjasper1 amd64 1.900.1-14 [160 kB] Get:56 http://localhost/debian/ unstable/main liblcms1 amd64 1.19.dfsg-1.2 [113 kB] Get:57 http://localhost/debian/ unstable/main liblcms2-2 amd64 2.2+git20110628-2.2 [143 kB] Get:58 http://localhost/debian/ unstable/main libopenjpeg2 amd64 1.3+dfsg-4.6 [85.9 kB] Get:59 http://localhost/debian/ unstable/main libthai-data all 0.1.18-2 [154 kB] Get:60 http://localhost/debian/ unstable/main libthai0 amd64 0.1.18-2 [42.3 kB] Get:61 http://localhost/debian/ unstable/main libxft2 amd64 2.3.1-1 [61.0 kB] Get:62 http://localhost/debian/ unstable/main fontconfig amd64 2.9.0-7.1 [348 kB] Get:63 http://localhost/debian/ unstable/main libpango1.0-0 amd64 1.30.0-1 [461 kB] Get:64 http://localhost/debian/ unstable/main libpaper1 amd64 1.1.24+nmu2 [22.0 kB] Get:65 http://localhost/debian/ unstable/main libpoppler19 amd64 0.18.4-4 [1109 kB] Get:66 http://localhost/debian/ unstable/main libsm6 amd64 2:1.2.1-2 [34.2 kB] Get:67 http://localhost/debian/ unstable/main libxext6 amd64 2:1.3.1-2 [55.3 kB] Get:68 http://localhost/debian/ unstable/main libxt6 amd64 1:1.1.3-1 [211 kB] Get:69 http://localhost/debian/ unstable/main libxmu6 amd64 2:1.1.1-1 [66.6 kB] Get:70 http://localhost/debian/ unstable/main libxpm4 amd64 1:3.5.10-1 [49.4 kB] Get:71 http://localhost/debian/ unstable/main libxaw7 amd64 2:1.0.10-2 [226 kB] Get:72 http://localhost/debian/ unstable/main tex-common all 3.15 [640 kB] Get:73 http://localhost/debian/ unstable/main libkpathsea6 amd64 2012.20120628-4 [164 kB] Get:74 http://localhost/debian/ unstable/main luatex amd64 0.70.1.20120524-3 [2438 kB] Get:75 http://localhost/debian/ unstable/main poppler-data all 0.4.6-2 [1484 kB] Get:76 http://localhost/debian/ unstable/main file amd64 5.11-2 [51.8 kB] Get:77 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-10 [154 kB] Get:78 http://localhost/debian/ unstable/main autotools-dev all 20120608.1 [73.0 kB] Get:79 http://localhost/debian/ unstable/main libbison-dev amd64 2:2.5.dfsg-3 [289 kB] Get:80 http://localhost/debian/ unstable/main bison amd64 2:2.5.dfsg-3 [688 kB] Get:81 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:82 http://localhost/debian/ unstable/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB] Get:83 http://localhost/debian/ unstable/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB] Get:84 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-10 [1815 kB] Get:85 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:86 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:87 http://localhost/debian/ unstable/main debhelper all 9.20120909 [705 kB] Get:88 http://localhost/debian/ unstable/main doxygen amd64 1.8.1.2-1 [2571 kB] Get:89 http://localhost/debian/ unstable/main ed amd64 1.6-2 [57.6 kB] Get:90 http://localhost/debian/ unstable/main libcdt4 amd64 2.26.3-12 [59.4 kB] Get:91 http://localhost/debian/ unstable/main libcgraph5 amd64 2.26.3-12 [87.3 kB] Get:92 http://localhost/debian/ unstable/main libgraph4 amd64 2.26.3-12 [73.4 kB] Get:93 http://localhost/debian/ unstable/main libpathplan4 amd64 2.26.3-12 [64.7 kB] Get:94 http://localhost/debian/ unstable/main libxdot4 amd64 2.26.3-12 [53.8 kB] Get:95 http://localhost/debian/ unstable/main libgvc5 amd64 2.26.3-12 [558 kB] Get:96 http://localhost/debian/ unstable/main libgvpr1 amd64 2.26.3-12 [243 kB] Get:97 http://localhost/debian/ unstable/main graphviz amd64 2.26.3-12 [375 kB] Get:98 http://localhost/debian/ unstable/main libgraphite3 amd64 1:2.3.1-0.2 [197 kB] Get:99 http://localhost/debian/ unstable/main libijs-0.35 amd64 0.35-8 [20.4 kB] Get:100 http://localhost/debian/ unstable/main libjbig2dec0 amd64 0.11+20120125-1 [51.8 kB] Get:101 http://localhost/debian/ unstable/main libgs9-common all 9.05~dfsg-6.3 [1977 kB] Get:102 http://localhost/debian/ unstable/main libgs9 amd64 9.05~dfsg-6.3 [1845 kB] Get:103 http://localhost/debian/ unstable/main libptexenc1 amd64 2012.20120628-4 [55.9 kB] Get:104 http://localhost/debian/ unstable/main texlive-common all 2012.20120611-5 [200 kB] Get:105 http://localhost/debian/ unstable/main texlive-binaries amd64 2012.20120628-4 [17.3 MB] Get:106 http://localhost/debian/ unstable/main texlive-doc-base all 2012.20120611-1 [1651 kB] Get:107 http://localhost/debian/ unstable/main xdg-utils all 1.1.0~rc1+git20111210-6 [83.7 kB] Get:108 http://localhost/debian/ unstable/main libpaper-utils amd64 1.1.24+nmu2 [18.3 kB] Get:109 http://localhost/debian/ unstable/main texlive-base all 2012.20120611-5 [14.2 MB] Get:110 http://localhost/debian/ unstable/main texlive-latex-base all 2012.20120611-5 [894 kB] Get:111 http://localhost/debian/ unstable/main texlive-latex-recommended all 2012.20120611-5 [6779 kB] Get:112 http://localhost/debian/ unstable/main latex-xcolor all 2.11-1.1 [610 kB] Get:113 http://localhost/debian/ unstable/main librostlab3 amd64 1.0.20-2 [5968 B] Get:114 http://localhost/debian/ unstable/main librostlab3-dev amd64 1.0.20-2 [13.6 kB] Get:115 http://localhost/debian/ unstable/main preview-latex-style all 11.87-1 [317 kB] Get:116 http://localhost/debian/ unstable/main ttf-marvosym all 0.1+dfsg-2 [46.8 kB] Get:117 http://localhost/debian/ unstable/main texlive-fonts-recommended all 2012.20120611-5 [5486 kB] Get:118 http://localhost/debian/ unstable/main texlive-pictures all 2012.20120611-5 [2276 kB] Get:119 http://localhost/debian/ unstable/main texlive-latex-extra all 2012.20120611-2 [6397 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 92.0 MB in 3s (30.3 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14674 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-1_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.1-2_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgpg-error0:amd64. Unpacking libgpg-error0:amd64 (from .../libgpg-error0_1.10-3.1_amd64.deb) ... Selecting previously unselected package libgcrypt11:amd64. Unpacking libgcrypt11:amd64 (from .../libgcrypt11_1.5.0-3_amd64.deb) ... Selecting previously unselected package libp11-kit0:amd64. Unpacking libp11-kit0:amd64 (from .../libp11-kit0_0.12-3_amd64.deb) ... Selecting previously unselected package libtasn1-3:amd64. Unpacking libtasn1-3:amd64 (from .../libtasn1-3_2.13-2_amd64.deb) ... Selecting previously unselected package libgnutls26:amd64. Unpacking libgnutls26:amd64 (from .../libgnutls26_2.12.20-3_amd64.deb) ... Selecting previously unselected package libkeyutils1:amd64. Unpacking libkeyutils1:amd64 (from .../libkeyutils1_1.5.5-4_amd64.deb) ... Selecting previously unselected package libkrb5support0:amd64. Unpacking libkrb5support0:amd64 (from .../libkrb5support0_1.10.1+dfsg-3_amd64.deb) ... Selecting previously unselected package libk5crypto3:amd64. Unpacking libk5crypto3:amd64 (from .../libk5crypto3_1.10.1+dfsg-3_amd64.deb) ... Selecting previously unselected package libkrb5-3:amd64. Unpacking libkrb5-3:amd64 (from .../libkrb5-3_1.10.1+dfsg-3_amd64.deb) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Unpacking libgssapi-krb5-2:amd64 (from .../libgssapi-krb5-2_1.10.1+dfsg-3_amd64.deb) ... Selecting previously unselected package libidn11:amd64. Unpacking libidn11:amd64 (from .../libidn11_1.25-2_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7_amd64.deb) ... Selecting previously unselected package libsigsegv2. Unpacking libsigsegv2 (from .../libsigsegv2_2.9-4_amd64.deb) ... Selecting previously unselected package m4. Unpacking m4 (from .../archives/m4_1.4.16-4_amd64.deb) ... Selecting previously unselected package flex. Unpacking flex (from .../flex_2.5.35-10.1_amd64.deb) ... Selecting previously unselected package libavahi-common-data:amd64. 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Unpacking sbuild-build-depends-librostlab-blast-dummy (from .../sbuild-build-depends-librostlab-blast-dummy.deb) ... Processing triggers for mime-support ... Setting up libpipeline1:amd64 (1.2.2-1) ... Setting up groff-base (1.22.1-2) ... Setting up bsdmainutils (9.0.4) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.3-3) ... Building database of manual pages ... Setting up libasprintf0c2:amd64 (0.18.1.1-10) ... Setting up libgpg-error0:amd64 (1.10-3.1) ... Setting up libgcrypt11:amd64 (1.5.0-3) ... Setting up libp11-kit0:amd64 (0.12-3) ... Setting up libtasn1-3:amd64 (2.13-2) ... Setting up libgnutls26:amd64 (2.12.20-3) ... Setting up libkeyutils1:amd64 (1.5.5-4) ... Setting up libkrb5support0:amd64 (1.10.1+dfsg-3) ... Setting up libk5crypto3:amd64 (1.10.1+dfsg-3) ... Setting up libkrb5-3:amd64 (1.10.1+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.10.1+dfsg-3) ... Setting up libidn11:amd64 (1.25-2) ... Setting up libmagic1:amd64 (5.11-2) ... Setting up libpcre3:amd64 (1:8.31-2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7) ... Setting up libsigsegv2 (2.9-4) ... Setting up m4 (1.4.16-4) ... Setting up flex (2.5.35-10.1) ... Setting up libavahi-common-data:amd64 (0.6.31-1) ... Setting up libavahi-common3:amd64 (0.6.31-1) ... Setting up libdbus-1-3:amd64 (1.6.8-1) ... Setting up libavahi-client3:amd64 (0.6.31-1) ... Setting up libfreetype6:amd64 (2.4.9-1.1) ... Setting up ttf-dejavu-core (2.33-3) ... Setting up fontconfig-config (2.9.0-7.1) ... Setting up libfontconfig1:amd64 (2.9.0-7.1) ... Setting up libpixman-1-0:amd64 (0.26.0-3) ... Setting up libpng12-0:amd64 (1.2.49-3) ... Setting up libxau6:amd64 (1:1.0.7-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.8.1-2) ... Setting up libx11-data (2:1.5.0-1) ... Setting up libx11-6:amd64 (2:1.5.0-1) ... Setting up libxcb-render0:amd64 (1.8.1-2) ... Setting up libxcb-shm0:amd64 (1.8.1-2) ... Setting up libxrender1:amd64 (1:0.9.7-1) ... Setting up libcairo2:amd64 (1.12.2-2.1) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.6-2) ... Setting up libcups2:amd64 (1.5.3-2.14) ... Setting up libjpeg8:amd64 (8d-1) ... Setting up libjbig0:amd64 (2.0-2) ... Setting up libtiff4:amd64 (3.9.6-11) ... Setting up libcupsimage2:amd64 (1.5.3-2.14) ... Setting up libdatrie1:amd64 (0.2.5-3) ... Setting up libgd2-noxpm:amd64 (2.0.36~rc1~dfsg-6.1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-10) ... Setting up x11-common (1:7.7+1) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:amd64 (2:1.0.8-2) ... Setting up libjasper1:amd64 (1.900.1-14) ... Setting up liblcms1:amd64 (1.19.dfsg-1.2) ... Setting up liblcms2-2:amd64 (2.2+git20110628-2.2) ... Setting up libopenjpeg2:amd64 (1.3+dfsg-4.6) ... Setting up libthai-data (0.1.18-2) ... Setting up libthai0:amd64 (0.1.18-2) ... Setting up libxft2:amd64 (2.3.1-1) ... Setting up fontconfig (2.9.0-7.1) ... Regenerating fonts cache... done. Setting up libpango1.0-0:amd64 (1.30.0-1) ... Setting up libpaper1:amd64 (1.1.24+nmu2) ... Creating config file /etc/papersize with new version Setting up libpoppler19:amd64 (0.18.4-4) ... Setting up libsm6:amd64 (2:1.2.1-2) ... Setting up libxext6:amd64 (2:1.3.1-2) ... Setting up libxt6:amd64 (1:1.1.3-1) ... Setting up libxmu6:amd64 (2:1.1.1-1) ... Setting up libxpm4:amd64 (1:3.5.10-1) ... Setting up libxaw7:amd64 (2:1.0.10-2) ... Setting up tex-common (3.15) ... Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up libkpathsea6 (2012.20120628-4) ... Setting up luatex (0.70.1.20120524-3) ... texlive-base is not ready, cannot create formats Setting up poppler-data (0.4.6-2) ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-10) ... Setting up autotools-dev (20120608.1) ... Setting up libbison-dev:amd64 (2:2.5.dfsg-3) ... Setting up bison (2:2.5.dfsg-3) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Setting up doxygen (1.8.1.2-1) ... Setting up ed (1.6-2) ... Setting up libcdt4 (2.26.3-12) ... Setting up libcgraph5 (2.26.3-12) ... Setting up libgraph4 (2.26.3-12) ... Setting up libpathplan4 (2.26.3-12) ... Setting up libxdot4 (2.26.3-12) ... Setting up libgvc5 (2.26.3-12) ... Setting up libgvpr1 (2.26.3-12) ... Setting up graphviz (2.26.3-12) ... Setting up libgraphite3 (1:2.3.1-0.2) ... Setting up libijs-0.35 (0.35-8) ... Setting up libjbig2dec0 (0.11+20120125-1) ... Setting up libgs9-common (9.05~dfsg-6.3) ... Setting up libgs9 (9.05~dfsg-6.3) ... Setting up libptexenc1 (2012.20120628-4) ... Setting up texlive-common (2012.20120611-5) ... Setting up texlive-binaries (2012.20120628-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Building format(s) --refresh. This may take some time... done. Setting up texlive-doc-base (2012.20120611-1) ... Setting up xdg-utils (1.1.0~rc1+git20111210-6) ... Setting up libpaper-utils (1.1.24+nmu2) ... Setting up librostlab3 (1.0.20-2) ... Setting up librostlab3-dev (1.0.20-2) ... Setting up preview-latex-style (11.87-1) ... Setting up ttf-marvosym (0.1+dfsg-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2012.20120611-5) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Running mktexlsr. This may take some time... done. Building format(s) --all. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-fonts-recommended (2012.20120611-5) ... Setting up texlive-pictures (2012.20120611-5) ... Setting up texlive-latex-base (2012.20120611-5) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-latex-recommended (2012.20120611-5) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up latex-xcolor (2.11-1.1) ... Setting up texlive-latex-extra (2012.20120611-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up sbuild-build-depends-librostlab-blast-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 g++-4.7_4.7.2-19 gcc-4.6_4.6.3-15 gcc-4.7_4.7.2-19 libc6-dev_2.16-0experimental1 libstdc++6_4.8-20130127-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 linux-libc-dev_3.2.35-2 Package versions: apt_0.9.7.7 autotools-dev_20120608.1 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 binutils_2.22-7.1 bison_2:2.5.dfsg-3 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 clang_3.2-1~exp5 clang-3.2_3.2-1~exp5 compiler-rt_3.2-1~exp5 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.6_4.6.3-15 cpp-4.7_4.7.2-19 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffutils_1:3.2-7 doxygen_1.8.1.2-1 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 ed_1.6-2 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 flex_2.5.35-10.1 fontconfig_2.9.0-7.1 fontconfig-config_2.9.0-7.1 g++_4:4.7.2-1 g++-4.6_4.6.3-15 g++-4.7_4.7.2-19 gcc_4:4.7.2-1 gcc-4.4-base_4.4.7-3 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7_4.7.2-19 gcc-4.7-base_4.7.2-19 gcc-4.8-base_4.8-20130127-1 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 graphviz_2.26.3-12 grep_2.14-1 groff-base_1.22.1-2 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-39 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 latex-xcolor_2.11-1.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libbison-dev_2:2.5.dfsg-3 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.16-0experimental1 libc6_2.16-0experimental1 libc6-dev_2.16-0experimental1 libcairo2_1.12.2-2.1 libcdt4_2.26.3-12 libcgraph5_2.26.3-12 libclang-common-dev_3.2-1~exp5 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libcups2_1.5.3-2.14 libcupsimage2_1.5.3-2.14 libdatrie1_0.2.5-3 libdb5.1_5.1.29-5 libdbus-1-3_1.6.8-1 libdpkg-perl_1.16.9 libexpat1_2.1.0-2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libfontconfig1_2.9.0-7.1 libfreetype6_2.4.9-1.1 libgc1c2_1:7.1-9.1 libgcc-4.7-dev_4.7.2-19 libgcc1_1:4.8-20130127-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-6.1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-3 libgomp1_4.8-20130127-1 libgpg-error0_1.10-3.1 libgpm2_1.20.4-6 libgraph4_2.26.3-12 libgraphite3_1:2.3.1-0.2 libgs9_9.05~dfsg-6.3 libgs9-common_9.05~dfsg-6.3 libgssapi-krb5-2_1.10.1+dfsg-3 libgvc5_2.26.3-12 libgvpr1_2.26.3-12 libice6_2:1.0.8-2 libidn11_1.25-2 libijs-0.35_0.35-8 libitm1_4.8-20130127-1 libjasper1_1.900.1-14 libjbig0_2.0-2 libjbig2dec0_0.11+20120125-1 libjpeg8_8d-1 libk5crypto3_1.10.1+dfsg-3 libkeyutils1_1.5.5-4 libkpathsea6_2012.20120628-4 libkrb5-3_1.10.1+dfsg-3 libkrb5support0_1.10.1+dfsg-3 liblcms1_1.19.dfsg-1.2 liblcms2-2_2.2+git20110628-2.2 libllvm3.2_3.2-2 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9+20130119-1 libncursesw5_5.9+20130119-1 libobjc-4.7-dev_4.7.2-19 libobjc4_4.8-20130127-1 libopenjpeg2_1.3+dfsg-4.6 libp11-kit0_0.12-3 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpango1.0-0_1.30.0-1 libpaper-utils_1.1.24+nmu2 libpaper1_1.1.24+nmu2 libpathplan4_2.26.3-12 libpcre3_1:8.31-2 libpipeline1_1.2.2-1 libpixman-1-0_0.26.0-3 libpng12-0_1.2.49-3 libpoppler19_0.18.4-4 libptexenc1_2012.20120628-4 libpython2.7-minimal_2.7.3-15 libpython2.7-stdlib_2.7.3-15 libquadmath0_4.8-20130127-1 libreadline6_6.2+dfsg-0.1 librostlab3_1.0.20-2 librostlab3-dev_1.0.20-2 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsigsegv2_2.9-4 libslang2_2.2.4-15 libsm6_2:1.2.1-2 libsqlite3-0_3.7.15.2-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.8-20130127-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 libswitch-perl_2.16-2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.18-2 libthai0_0.1.18-2 libtiff4_3.9.6-11 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130119-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxau6_1:1.0.7-1 libxaw7_2:1.0.10-2 libxcb-render0_1.8.1-2 libxcb-shm0_1.8.1-2 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1 libxdot4_2.26.3-12 libxext6_2:1.3.1-2 libxft2_2.3.1-1 libxml2_2.8.0+dfsg1-7 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender1_1:0.9.7-1 libxt6_1:1.1.3-1 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 luatex_0.70.1.20120524-3 m4_1.4.16-4 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mime-support_3.53~experimental2 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-17 perl-base_5.14.2-17 perl-modules_5.14.2-17 po-debconf_1.0.16+nmu2 poppler-data_0.4.6-2 preview-latex-style_11.87-1 python_2.7.3-10 python-minimal_2.7.3-10 python2.7_2.7.3-15 python2.7-minimal_2.7.3-15 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-librostlab-blast-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-39 sysvinit_2.88dsf-39 sysvinit-utils_2.88dsf-39 tar_1.26+dfsg-0.1 tex-common_3.15 texlive-base_2012.20120611-5 texlive-binaries_2012.20120628-4 texlive-common_2012.20120611-5 texlive-doc-base_2012.20120611-1 texlive-fonts-recommended_2012.20120611-5 texlive-latex-base_2012.20120611-5 texlive-latex-extra_2012.20120611-2 texlive-latex-recommended_2012.20120611-5 texlive-pictures_2012.20120611-5 ttf-dejavu-core_2.33-3 ttf-marvosym_0.1+dfsg-2 tzdata_2012j-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.3 vim_2:7.3.547-6 vim-common_2:7.3.547-6 vim-runtime_2:7.3.547-6 x11-common_1:7.7+1 xdg-utils_1.1.0~rc1+git20111210-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sun Dec 16 22:00:15 2012 UTC using RSA key ID 9A0C52FA gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./librostlab-blast_1.0.1-2.dsc dpkg-source: info: extracting librostlab-blast in librostlab-blast-1.0.1 dpkg-source: info: unpacking librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: unpacking librostlab-blast_1.0.1-2.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-68619075-adfa-45e8-a180-0207d4e9da80 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package librostlab-blast dpkg-buildpackage: source version 1.0.1-2 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build librostlab-blast-1.0.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_clean --parallel rm -f lib/librostlab-blast.tag make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_configure --parallel -- --enable-doxygen-dot --enable-doxygen-pdf configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for bison... bison -y checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking rostlab/aux_functions.h usability... no checking rostlab/aux_functions.h presence... yes configure: WARNING: rostlab/aux_functions.h: present but cannot be compiled configure: WARNING: rostlab/aux_functions.h: check for missing prerequisite headers? configure: WARNING: rostlab/aux_functions.h: see the Autoconf documentation configure: WARNING: rostlab/aux_functions.h: section "Present But Cannot Be Compiled" configure: WARNING: rostlab/aux_functions.h: proceeding with the compiler's result configure: WARNING: ## ------------------------------------------------------------------------------------------- ## configure: WARNING: ## Report this to https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast ## configure: WARNING: ## ------------------------------------------------------------------------------------------- ## checking for rostlab/aux_functions.h... no required header is missing - please install librostlab ==> config.log <== This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by librostlab-blast configure 1.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libexecdir=${prefix}/lib/librostlab-blast --disable-maintainer-mode --disable-dependency-tracking --enable-doxygen-dot --enable-doxygen-pdf ## --------- ## ## Platform. ## ## --------- ## hostname = ip-10-29-139-51 uname -m = x86_64 uname -r = 2.6.32-5-xen-amd64 uname -s = Linux uname -v = #1 SMP Sun Sep 23 13:49:30 UTC 2012 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /usr/games ## ----------- ## ## Core tests. ## ## ----------- ## configure:2465: checking for a BSD-compatible install configure:2533: result: /usr/bin/install -c configure:2544: checking whether build environment is sane configure:2594: result: yes configure:2735: checking for a thread-safe mkdir -p configure:2774: result: /bin/mkdir -p configure:2787: checking for gawk configure:2817: result: no configure:2787: checking for mawk configure:2803: found /usr/bin/mawk configure:2814: result: mawk configure:2825: checking whether make sets $(MAKE) configure:2847: result: yes configure:2976: checking for gcc configure:2992: found /usr/bin/gcc configure:3003: result: gcc configure:3232: checking for C compiler version configure:3241: gcc --version >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3252: $? = 0 configure:3241: gcc -v >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:3252: $? = 0 configure:3241: gcc -V >&5 clang: error: argument to '-V' is missing (expected 1 value) clang: error: no input files configure:3252: $? = 1 configure:3241: gcc -qversion >&5 clang: error: no input files configure:3252: $? = 1 configure:3272: checking whether the C compiler works configure:3294: gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c >&5 configure:3298: $? = 0 configure:3346: result: yes configure:3349: checking for C compiler default output file name configure:3351: result: a.out configure:3357: checking for suffix of executables configure:3364: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c >&5 configure:3368: $? = 0 configure:3390: result: configure:3412: checking whether we are cross compiling configure:3420: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c >&5 configure:3424: $? = 0 configure:3431: ./conftest configure:3435: $? = 0 configure:3450: result: no configure:3455: checking for suffix of object files configure:3477: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3481: $? = 0 configure:3502: result: o configure:3506: checking whether we are using the GNU C compiler configure:3525: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3525: $? = 0 configure:3534: result: yes configure:3543: checking whether gcc accepts -g configure:3563: gcc -c -g -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3563: $? = 0 configure:3604: result: yes configure:3621: checking for gcc option to accept ISO C89 configure:3684: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3684: $? = 0 configure:3697: result: none needed configure:3728: checking for style of include used by make configure:3756: result: GNU configure:3782: checking dependency style of gcc configure:3893: result: none configure:3966: checking for g++ configure:3982: found /usr/bin/g++ configure:3993: result: g++ configure:4020: checking for C++ compiler version configure:4029: g++ --version >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:4040: $? = 0 configure:4029: g++ -v >&5 Debian clang version 3.2-1~exp5 (tags/RELEASE_32/final) (based on LLVM 3.2) Target: x86_64-pc-linux-gnu Thread model: posix configure:4040: $? = 0 configure:4029: g++ -V >&5 clang: error: argument to '-V' is missing (expected 1 value) clang: error: no input files configure:4040: $? = 1 configure:4029: g++ -qversion >&5 clang: error: no input files configure:4040: $? = 1 configure:4044: checking whether we are using the GNU C++ compiler configure:4063: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:4063: $? = 0 configure:4072: result: yes configure:4081: checking whether g++ accepts -g configure:4101: g++ -c -g -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:4101: $? = 0 configure:4142: result: yes configure:4167: checking dependency style of g++ configure:4278: result: none configure:4322: checking build system type configure:4336: result: x86_64-pc-linux-gnu configure:4356: checking host system type configure:4369: result: x86_64-pc-linux-gnu configure:4410: checking how to print strings configure:4437: result: printf configure:4458: checking for a sed that does not truncate output configure:4522: result: /bin/sed configure:4540: checking for grep that handles long lines and -e configure:4598: result: /bin/grep configure:4603: checking for egrep configure:4665: result: /bin/grep -E configure:4670: checking for fgrep configure:4732: result: /bin/grep -F configure:4767: checking for ld used by gcc configure:4834: result: /usr/bin/ld configure:4841: checking if the linker (/usr/bin/ld) is GNU ld configure:4856: result: yes configure:4868: checking for BSD- or MS-compatible name lister (nm) configure:4917: result: /usr/bin/nm -B configure:5047: checking the name lister (/usr/bin/nm -B) interface configure:5054: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:5057: /usr/bin/nm -B "conftest.o" configure:5060: output 0000000000000000 B some_variable configure:5067: result: BSD nm configure:5070: checking whether ln -s works configure:5074: result: yes configure:5082: checking the maximum length of command line arguments configure:5213: result: 3458764513820540925 configure:5230: checking whether the shell understands some XSI constructs configure:5240: result: yes configure:5244: checking whether the shell understands "+=" configure:5250: result: yes configure:5285: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format configure:5325: result: func_convert_file_noop configure:5332: checking how to convert x86_64-pc-linux-gnu file names to toolchain format configure:5352: result: func_convert_file_noop configure:5359: checking for /usr/bin/ld option to reload object files configure:5366: result: -r configure:5440: checking for objdump configure:5456: found /usr/bin/objdump configure:5467: result: objdump configure:5499: checking how to recognize dependent libraries configure:5697: result: pass_all configure:5782: checking for dlltool configure:5812: result: no configure:5842: checking how to associate runtime and link libraries configure:5869: result: printf %s\n configure:5930: checking for ar configure:5946: found /usr/bin/ar configure:5957: result: ar configure:5994: checking for archiver @FILE support configure:6011: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:6011: $? = 0 configure:6014: ar cru libconftest.a @conftest.lst >&5 configure:6017: $? = 0 configure:6022: ar cru libconftest.a @conftest.lst >&5 ar: conftest.o: No such file or directory configure:6025: $? = 1 configure:6037: result: @ configure:6095: checking for strip configure:6111: found /usr/bin/strip configure:6122: result: strip configure:6194: checking for ranlib configure:6210: found /usr/bin/ranlib configure:6221: result: ranlib configure:6323: checking command to parse /usr/bin/nm -B output from gcc object configure:6443: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:6446: $? = 0 configure:6450: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm configure:6453: $? = 0 configure:6519: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c conftstm.o >&5 configure:6522: $? = 0 configure:6560: result: ok configure:6597: checking for sysroot configure:6627: result: no configure:6704: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:6707: $? = 0 configure:6890: checking for mt configure:6920: result: no configure:6940: checking if : is a manifest tool configure:6946: : '-?' configure:6954: result: no configure:7596: checking how to run the C preprocessor configure:7627: gcc -E -D_FORTIFY_SOURCE=2 conftest.c configure:7627: $? = 0 configure:7641: gcc -E -D_FORTIFY_SOURCE=2 conftest.c conftest.c:11:10: fatal error: 'ac_nonexistent.h' file not found #include ^ 1 error generated. configure:7641: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | /* end confdefs.h. */ | #include configure:7666: result: gcc -E configure:7686: gcc -E -D_FORTIFY_SOURCE=2 conftest.c configure:7686: $? = 0 configure:7700: gcc -E -D_FORTIFY_SOURCE=2 conftest.c conftest.c:11:10: fatal error: 'ac_nonexistent.h' file not found #include ^ 1 error generated. configure:7700: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | /* end confdefs.h. */ | #include configure:7729: checking for ANSI C header files configure:7749: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7749: $? = 0 configure:7822: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c >&5 configure:7822: $? = 0 configure:7822: ./conftest configure:7822: $? = 0 configure:7833: result: yes configure:7846: checking for sys/types.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for sys/stat.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for stdlib.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for string.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for memory.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for strings.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for inttypes.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for stdint.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7846: checking for unistd.h configure:7846: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7846: $? = 0 configure:7846: result: yes configure:7860: checking for dlfcn.h configure:7860: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:7860: $? = 0 configure:7860: result: yes configure:8077: checking for objdir configure:8092: result: .libs configure:8363: checking if gcc supports -fno-rtti -fno-exceptions configure:8381: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fno-rtti -fno-exceptions conftest.c >&5 configure:8385: $? = 0 configure:8398: result: yes configure:8725: checking for gcc option to produce PIC configure:8732: result: -fPIC -DPIC configure:8740: checking if gcc PIC flag -fPIC -DPIC works configure:8758: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DPIC -DPIC conftest.c >&5 configure:8762: $? = 0 configure:8775: result: yes configure:8804: checking if gcc static flag -static works configure:8832: result: yes configure:8847: checking if gcc supports -c -o file.o configure:8868: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -o out/conftest2.o conftest.c >&5 configure:8872: $? = 0 configure:8894: result: yes configure:8902: checking if gcc supports -c -o file.o configure:8949: result: yes configure:8982: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:10139: result: yes configure:10176: checking whether -lc should be explicitly linked in configure:10184: gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:10187: $? = 0 configure:10202: gcc -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1 configure:10205: $? = 0 configure:10219: result: no configure:10379: checking dynamic linker characteristics configure:10879: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-rpath -Wl,/foo conftest.c >&5 configure:10879: $? = 0 configure:11113: result: GNU/Linux ld.so configure:11220: checking how to hardcode library paths into programs configure:11245: result: immediate configure:11785: checking whether stripping libraries is possible configure:11790: result: yes configure:11825: checking if libtool supports shared libraries configure:11827: result: yes configure:11830: checking whether to build shared libraries configure:11851: result: yes configure:11854: checking whether to build static libraries configure:11858: result: yes configure:11881: checking how to run the C++ preprocessor configure:11908: g++ -E -D_FORTIFY_SOURCE=2 conftest.cpp configure:11908: $? = 0 configure:11922: g++ -E -D_FORTIFY_SOURCE=2 conftest.cpp conftest.cpp:23:10: fatal error: 'ac_nonexistent.h' file not found #include ^ 1 error generated. configure:11922: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:11947: result: g++ -E configure:11967: g++ -E -D_FORTIFY_SOURCE=2 conftest.cpp configure:11967: $? = 0 configure:11981: g++ -E -D_FORTIFY_SOURCE=2 conftest.cpp conftest.cpp:23:10: fatal error: 'ac_nonexistent.h' file not found #include ^ 1 error generated. configure:11981: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:12150: checking for ld used by g++ configure:12217: result: /usr/bin/ld -m elf_x86_64 configure:12224: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld configure:12239: result: yes configure:12294: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:13296: result: yes configure:13332: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 configure:13335: $? = 0 configure:13855: checking for g++ option to produce PIC configure:13862: result: -fPIC -DPIC configure:13870: checking if g++ PIC flag -fPIC -DPIC works configure:13888: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DPIC -DPIC conftest.cpp >&5 configure:13892: $? = 0 configure:13905: result: yes configure:13928: checking if g++ static flag -static works configure:13956: result: yes configure:13968: checking if g++ supports -c -o file.o configure:13989: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -o out/conftest2.o conftest.cpp >&5 configure:13993: $? = 0 configure:14015: result: yes configure:14020: checking if g++ supports -c -o file.o configure:14067: result: yes configure:14097: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:14136: result: yes configure:14277: checking dynamic linker characteristics configure:14945: result: GNU/Linux ld.so configure:14998: checking how to hardcode library paths into programs configure:15023: result: immediate configure:15088: checking for bison configure:15104: found /usr/bin/bison configure:15115: result: bison -y configure:15131: checking for flex configure:15147: found /usr/bin/flex configure:15158: result: flex configure:15196: flex conftest.l configure:15200: $? = 0 configure:15202: checking lex output file root configure:15216: result: lex.yy configure:15221: checking lex library configure:15235: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c >&5 /tmp/conftest-gDu231.o: In function `yylex': /«PKGBUILDDIR»/lex.yy.c:882: undefined reference to `yywrap' /tmp/conftest-gDu231.o: In function `input': /«PKGBUILDDIR»/lex.yy.c:1183: undefined reference to `yywrap' /tmp/conftest-gDu231.o: In function `main': /«PKGBUILDDIR»/conftest.l:18: undefined reference to `yywrap' clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:15235: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #line 3 "lex.yy.c" | | #define YY_INT_ALIGNED short int | | /* A lexical scanner generated by flex */ | | #define FLEX_SCANNER | #define YY_FLEX_MAJOR_VERSION 2 | #define YY_FLEX_MINOR_VERSION 5 | #define YY_FLEX_SUBMINOR_VERSION 35 | #if YY_FLEX_SUBMINOR_VERSION > 0 | #define FLEX_BETA | #endif | | /* First, we deal with platform-specific or compiler-specific issues. */ | | /* begin standard C headers. */ | #include | #include | #include | #include | | /* end standard C headers. */ | | /* flex integer type definitions */ | | #ifndef FLEXINT_H | #define FLEXINT_H | | /* C99 systems have . Non-C99 systems may or may not. */ | | #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L | | /* C99 says to define __STDC_LIMIT_MACROS before including stdint.h, | * if you want the limit (max/min) macros for int types. | */ | #ifndef __STDC_LIMIT_MACROS | #define __STDC_LIMIT_MACROS 1 | #endif | | #include | typedef int8_t flex_int8_t; | typedef uint8_t flex_uint8_t; | typedef int16_t flex_int16_t; | typedef uint16_t flex_uint16_t; | typedef int32_t flex_int32_t; | typedef uint32_t flex_uint32_t; | #else | typedef signed char flex_int8_t; | typedef short int flex_int16_t; | typedef int flex_int32_t; | typedef unsigned char flex_uint8_t; | typedef unsigned short int flex_uint16_t; | typedef unsigned int flex_uint32_t; | | /* Limits of integral types. */ | #ifndef INT8_MIN | #define INT8_MIN (-128) | #endif | #ifndef INT16_MIN | #define INT16_MIN (-32767-1) | #endif | #ifndef INT32_MIN | #define INT32_MIN (-2147483647-1) | #endif | #ifndef INT8_MAX | #define INT8_MAX (127) | #endif | #ifndef INT16_MAX | #define INT16_MAX (32767) | #endif | #ifndef INT32_MAX | #define INT32_MAX (2147483647) | #endif | #ifndef UINT8_MAX | #define UINT8_MAX (255U) | #endif | #ifndef UINT16_MAX | #define UINT16_MAX (65535U) | #endif | #ifndef UINT32_MAX | #define UINT32_MAX (4294967295U) | #endif | | #endif /* ! C99 */ | | #endif /* ! FLEXINT_H */ | | #ifdef __cplusplus | | /* The "const" storage-class-modifier is valid. */ | #define YY_USE_CONST | | #else /* ! __cplusplus */ | | /* C99 requires __STDC__ to be defined as 1. */ | #if defined (__STDC__) | | #define YY_USE_CONST | | #endif /* defined (__STDC__) */ | #endif /* ! __cplusplus */ | | #ifdef YY_USE_CONST | #define yyconst const | #else | #define yyconst | #endif | | /* Returned upon end-of-file. */ | #define YY_NULL 0 | | /* Promotes a possibly negative, possibly signed char to an unsigned | * integer for use as an array index. If the signed char is negative, | * we want to instead treat it as an 8-bit unsigned char, hence the | * double cast. | */ | #define YY_SC_TO_UI(c) ((unsigned int) (unsigned char) c) | | /* Enter a start condition. This macro really ought to take a parameter, | * but we do it the disgusting crufty way forced on us by the ()-less | * definition of BEGIN. | */ | #define BEGIN (yy_start) = 1 + 2 * | | /* Translate the current start state into a value that can be later handed | * to BEGIN to return to the state. The YYSTATE alias is for lex | * compatibility. | */ | #define YY_START (((yy_start) - 1) / 2) | #define YYSTATE YY_START | | /* Action number for EOF rule of a given start state. */ | #define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1) | | /* Special action meaning "start processing a new file". */ | #define YY_NEW_FILE yyrestart(yyin ) | | #define YY_END_OF_BUFFER_CHAR 0 | | /* Size of default input buffer. */ | #ifndef YY_BUF_SIZE | #ifdef __ia64__ | /* On IA-64, the buffer size is 16k, not 8k. | * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case. | * Ditto for the __ia64__ case accordingly. | */ | #define YY_BUF_SIZE 32768 | #else | #define YY_BUF_SIZE 16384 | #endif /* __ia64__ */ | #endif | | /* The state buf must be large enough to hold one state per character in the main buffer. | */ | #define YY_STATE_BUF_SIZE ((YY_BUF_SIZE + 2) * sizeof(yy_state_type)) | | #ifndef YY_TYPEDEF_YY_BUFFER_STATE | #define YY_TYPEDEF_YY_BUFFER_STATE | typedef struct yy_buffer_state *YY_BUFFER_STATE; | #endif | | extern int yyleng; | | extern FILE *yyin, *yyout; | | #define EOB_ACT_CONTINUE_SCAN 0 | #define EOB_ACT_END_OF_FILE 1 | #define EOB_ACT_LAST_MATCH 2 | | #define YY_LESS_LINENO(n) | | /* Return all but the first "n" matched characters back to the input stream. */ | #define yyless(n) \ | do \ | { \ | /* Undo effects of setting up yytext. */ \ | int yyless_macro_arg = (n); \ | YY_LESS_LINENO(yyless_macro_arg);\ | *yy_cp = (yy_hold_char); \ | YY_RESTORE_YY_MORE_OFFSET \ | (yy_c_buf_p) = yy_cp = yy_bp + yyless_macro_arg - YY_MORE_ADJ; \ | YY_DO_BEFORE_ACTION; /* set up yytext again */ \ | } \ | while ( 0 ) | | #define unput(c) yyunput( c, (yytext_ptr) ) | | #ifndef YY_TYPEDEF_YY_SIZE_T | #define YY_TYPEDEF_YY_SIZE_T | typedef size_t yy_size_t; | #endif | | #ifndef YY_STRUCT_YY_BUFFER_STATE | #define YY_STRUCT_YY_BUFFER_STATE | struct yy_buffer_state | { | FILE *yy_input_file; | | char *yy_ch_buf; /* input buffer */ | char *yy_buf_pos; /* current position in input buffer */ | | /* Size of input buffer in bytes, not including room for EOB | * characters. | */ | yy_size_t yy_buf_size; | | /* Number of characters read into yy_ch_buf, not including EOB | * characters. | */ | int yy_n_chars; | | /* Whether we "own" the buffer - i.e., we know we created it, | * and can realloc() it to grow it, and should free() it to | * delete it. | */ | int yy_is_our_buffer; | | /* Whether this is an "interactive" input source; if so, and | * if we're using stdio for input, then we want to use getc() | * instead of fread(), to make sure we stop fetching input after | * each newline. | */ | int yy_is_interactive; | | /* Whether we're considered to be at the beginning of a line. | * If so, '^' rules will be active on the next match, otherwise | * not. | */ | int yy_at_bol; | | int yy_bs_lineno; /**< The line count. */ | int yy_bs_column; /**< The column count. */ | | /* Whether to try to fill the input buffer when we reach the | * end of it. | */ | int yy_fill_buffer; | | int yy_buffer_status; | | #define YY_BUFFER_NEW 0 | #define YY_BUFFER_NORMAL 1 | /* When an EOF's been seen but there's still some text to process | * then we mark the buffer as YY_EOF_PENDING, to indicate that we | * shouldn't try reading from the input source any more. We might | * still have a bunch of tokens to match, though, because of | * possible backing-up. | * | * When we actually see the EOF, we change the status to "new" | * (via yyrestart()), so that the user can continue scanning by | * just pointing yyin at a new input file. | */ | #define YY_BUFFER_EOF_PENDING 2 | | }; | #endif /* !YY_STRUCT_YY_BUFFER_STATE */ | | /* Stack of input buffers. */ | static size_t yy_buffer_stack_top = 0; /**< index of top of stack. */ | static size_t yy_buffer_stack_max = 0; /**< capacity of stack. */ | static YY_BUFFER_STATE * yy_buffer_stack = 0; /**< Stack as an array. */ | | /* We provide macros for accessing buffer states in case in the | * future we want to put the buffer states in a more general | * "scanner state". | * | * Returns the top of the stack, or NULL. | */ | #define YY_CURRENT_BUFFER ( (yy_buffer_stack) \ | ? (yy_buffer_stack)[(yy_buffer_stack_top)] \ | : NULL) | | /* Same as previous macro, but useful when we know that the buffer stack is not | * NULL or when we need an lvalue. For internal use only. | */ | #define YY_CURRENT_BUFFER_LVALUE (yy_buffer_stack)[(yy_buffer_stack_top)] | | /* yy_hold_char holds the character lost when yytext is formed. */ | static char yy_hold_char; | static int yy_n_chars; /* number of characters read into yy_ch_buf */ | int yyleng; | | /* Points to current character in buffer. */ | static char *yy_c_buf_p = (char *) 0; | static int yy_init = 0; /* whether we need to initialize */ | static int yy_start = 0; /* start state number */ | | /* Flag which is used to allow yywrap()'s to do buffer switches | * instead of setting up a fresh yyin. A bit of a hack ... | */ | static int yy_did_buffer_switch_on_eof; | | void yyrestart (FILE *input_file ); | void yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ); | YY_BUFFER_STATE yy_create_buffer (FILE *file,int size ); | void yy_delete_buffer (YY_BUFFER_STATE b ); | void yy_flush_buffer (YY_BUFFER_STATE b ); | void yypush_buffer_state (YY_BUFFER_STATE new_buffer ); | void yypop_buffer_state (void ); | | static void yyensure_buffer_stack (void ); | static void yy_load_buffer_state (void ); | static void yy_init_buffer (YY_BUFFER_STATE b,FILE *file ); | | #define YY_FLUSH_BUFFER yy_flush_buffer(YY_CURRENT_BUFFER ) | | YY_BUFFER_STATE yy_scan_buffer (char *base,yy_size_t size ); | YY_BUFFER_STATE yy_scan_string (yyconst char *yy_str ); | YY_BUFFER_STATE yy_scan_bytes (yyconst char *bytes,int len ); | | void *yyalloc (yy_size_t ); | void *yyrealloc (void *,yy_size_t ); | void yyfree (void * ); | | #define yy_new_buffer yy_create_buffer | | #define yy_set_interactive(is_interactive) \ | { \ | if ( ! YY_CURRENT_BUFFER ){ \ | yyensure_buffer_stack (); \ | YY_CURRENT_BUFFER_LVALUE = \ | yy_create_buffer(yyin,YY_BUF_SIZE ); \ | } \ | YY_CURRENT_BUFFER_LVALUE->yy_is_interactive = is_interactive; \ | } | | #define yy_set_bol(at_bol) \ | { \ | if ( ! YY_CURRENT_BUFFER ){\ | yyensure_buffer_stack (); \ | YY_CURRENT_BUFFER_LVALUE = \ | yy_create_buffer(yyin,YY_BUF_SIZE ); \ | } \ | YY_CURRENT_BUFFER_LVALUE->yy_at_bol = at_bol; \ | } | | #define YY_AT_BOL() (YY_CURRENT_BUFFER_LVALUE->yy_at_bol) | | /* Begin user sect3 */ | | typedef unsigned char YY_CHAR; | | FILE *yyin = (FILE *) 0, *yyout = (FILE *) 0; | | typedef int yy_state_type; | | extern int yylineno; | | int yylineno = 1; | | extern char *yytext; | #define yytext_ptr yytext | | static yy_state_type yy_get_previous_state (void ); | static yy_state_type yy_try_NUL_trans (yy_state_type current_state ); | static int yy_get_next_buffer (void ); | static void yy_fatal_error (yyconst char msg[] ); | | /* Done after the current pattern has been matched and before the | * corresponding action - sets up yytext. | */ | #define YY_DO_BEFORE_ACTION \ | (yytext_ptr) = yy_bp; \ | (yytext_ptr) -= (yy_more_len); \ | yyleng = (size_t) (yy_cp - (yytext_ptr)); \ | (yy_hold_char) = *yy_cp; \ | *yy_cp = '\0'; \ | (yy_c_buf_p) = yy_cp; | | #define YY_NUM_RULES 8 | #define YY_END_OF_BUFFER 9 | /* This struct is not used in this scanner, | but its presence is necessary. */ | struct yy_trans_info | { | flex_int32_t yy_verify; | flex_int32_t yy_nxt; | }; | static yyconst flex_int16_t yy_acclist[23] = | { 0, | 9, 7, 8, 8, 1, 7, 8, 2, 7, 8, | 3, 7, 8, 4, 7, 8, 5, 7, 8, 6, | 7, 8 | } ; | | static yyconst flex_int16_t yy_accept[14] = | { 0, | 1, 1, 1, 2, 4, 5, 8, 11, 14, 17, | 20, 23, 23 | } ; | | static yyconst flex_int32_t yy_ec[256] = | { 0, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 3, 4, 5, 6, | | 7, 8, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, | 1, 1, 1, 1, 1 | } ; | | static yyconst flex_int32_t yy_meta[9] = | { 0, | 1, 1, 1, 1, 1, 1, 1, 1 | } ; | | static yyconst flex_int16_t yy_base[13] = | { 0, | 0, 0, 9, 10, 10, 10, 10, 10, 10, 10, | 10, 10 | } ; | | static yyconst flex_int16_t yy_def[13] = | { 0, | 12, 1, 12, 12, 12, 12, 12, 12, 12, 12, | 12, 0 | } ; | | static yyconst flex_int16_t yy_nxt[19] = | { 0, | 4, 5, 6, 7, 8, 9, 10, 11, 12, 3, | 12, 12, 12, 12, 12, 12, 12, 12 | } ; | | static yyconst flex_int16_t yy_chk[19] = | { 0, | 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, | 12, 12, 12, 12, 12, 12, 12, 12 | } ; | | extern int yy_flex_debug; | int yy_flex_debug = 0; | | static yy_state_type *yy_state_buf=0, *yy_state_ptr=0; | static char *yy_full_match; | static int yy_lp; | #define REJECT \ | { \ | *yy_cp = (yy_hold_char); /* undo effects of setting up yytext */ \ | yy_cp = (yy_full_match); /* restore poss. backed-over text */ \ | ++(yy_lp); \ | goto find_rule; \ | } | | static int yy_more_flag = 0; | static int yy_more_len = 0; | #define yymore() ((yy_more_flag) = 1) | #define YY_MORE_ADJ (yy_more_len) | #define YY_RESTORE_YY_MORE_OFFSET | char *yytext; | #line 1 "conftest.l" | #line 477 "lex.yy.c" | | #define INITIAL 0 | | #ifndef YY_NO_UNISTD_H | /* Special case for "unistd.h", since it is non-ANSI. We include it way | * down here because we want the user's section 1 to have been scanned first. | * The user has a chance to override it with an option. | */ | #include | #endif | | #ifndef YY_EXTRA_TYPE | #define YY_EXTRA_TYPE void * | #endif | | static int yy_init_globals (void ); | | /* Accessor methods to globals. | These are made visible to non-reentrant scanners for convenience. */ | | int yylex_destroy (void ); | | int yyget_debug (void ); | | void yyset_debug (int debug_flag ); | | YY_EXTRA_TYPE yyget_extra (void ); | | void yyset_extra (YY_EXTRA_TYPE user_defined ); | | FILE *yyget_in (void ); | | void yyset_in (FILE * in_str ); | | FILE *yyget_out (void ); | | void yyset_out (FILE * out_str ); | | int yyget_leng (void ); | | char *yyget_text (void ); | | int yyget_lineno (void ); | | void yyset_lineno (int line_number ); | | /* Macros after this point can all be overridden by user definitions in | * section 1. | */ | | #ifndef YY_SKIP_YYWRAP | #ifdef __cplusplus | extern "C" int yywrap (void ); | #else | extern int yywrap (void ); | #endif | #endif | | static void yyunput (int c,char *buf_ptr ); | | #ifndef yytext_ptr | static void yy_flex_strncpy (char *,yyconst char *,int ); | #endif | | #ifdef YY_NEED_STRLEN | static int yy_flex_strlen (yyconst char * ); | #endif | | #ifndef YY_NO_INPUT | | #ifdef __cplusplus | static int yyinput (void ); | #else | static int input (void ); | #endif | | #endif | | /* Amount of stuff to slurp up with each read. */ | #ifndef YY_READ_BUF_SIZE | #ifdef __ia64__ | /* On IA-64, the buffer size is 16k, not 8k */ | #define YY_READ_BUF_SIZE 16384 | #else | #define YY_READ_BUF_SIZE 8192 | #endif /* __ia64__ */ | #endif | | /* Copy whatever the last rule matched to the standard output. */ | #ifndef ECHO | /* This used to be an fputs(), but since the string might contain NUL's, | * we now use fwrite(). | */ | #define ECHO do { if (fwrite( yytext, yyleng, 1, yyout )) {} } while (0) | #endif | | /* Gets input and stuffs it into "buf". number of characters read, or YY_NULL, | * is returned in "result". | */ | #ifndef YY_INPUT | #define YY_INPUT(buf,result,max_size) \ | if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \ | { \ | int c = '*'; \ | size_t n; \ | for ( n = 0; n < max_size && \ | (c = getc( yyin )) != EOF && c != '\n'; ++n ) \ | buf[n] = (char) c; \ | if ( c == '\n' ) \ | buf[n++] = (char) c; \ | if ( c == EOF && ferror( yyin ) ) \ | YY_FATAL_ERROR( "input in flex scanner failed" ); \ | result = n; \ | } \ | else \ | { \ | errno=0; \ | while ( (result = fread(buf, 1, max_size, yyin))==0 && ferror(yyin)) \ | { \ | if( errno != EINTR) \ | { \ | YY_FATAL_ERROR( "input in flex scanner failed" ); \ | break; \ | } \ | errno=0; \ | clearerr(yyin); \ | } \ | }\ | \ | | #endif | | /* No semi-colon after return; correct usage is to write "yyterminate();" - | * we don't want an extra ';' after the "return" because that will cause | * some compilers to complain about unreachable statements. | */ | #ifndef yyterminate | #define yyterminate() return YY_NULL | #endif | | /* Number of entries by which start-condition stack grows. */ | #ifndef YY_START_STACK_INCR | #define YY_START_STACK_INCR 25 | #endif | | /* Report a fatal error. */ | #ifndef YY_FATAL_ERROR | #define YY_FATAL_ERROR(msg) yy_fatal_error( msg ) | #endif | | /* end tables serialization structures and prototypes */ | | /* Default declaration of generated scanner - a define so the user can | * easily add parameters. | */ | #ifndef YY_DECL | #define YY_DECL_IS_OURS 1 | | extern int yylex (void); | | #define YY_DECL int yylex (void) | #endif /* !YY_DECL */ | | /* Code executed at the beginning of each rule, after yytext and yyleng | * have been set up. | */ | #ifndef YY_USER_ACTION | #define YY_USER_ACTION | #endif | | /* Code executed at the end of each rule. */ | #ifndef YY_BREAK | #define YY_BREAK break; | #endif | | #define YY_RULE_SETUP \ | YY_USER_ACTION | | /** The main scanner function which does all the work. | */ | YY_DECL | { | register yy_state_type yy_current_state; | register char *yy_cp, *yy_bp; | register int yy_act; | | #line 1 "conftest.l" | | #line 666 "lex.yy.c" | | if ( !(yy_init) ) | { | (yy_init) = 1; | | #ifdef YY_USER_INIT | YY_USER_INIT; | #endif | | /* Create the reject buffer large enough to save one state per allowed character. */ | if ( ! (yy_state_buf) ) | (yy_state_buf) = (yy_state_type *)yyalloc(YY_STATE_BUF_SIZE ); | if ( ! (yy_state_buf) ) | YY_FATAL_ERROR( "out of dynamic memory in yylex()" ); | | if ( ! (yy_start) ) | (yy_start) = 1; /* first start state */ | | if ( ! yyin ) | yyin = stdin; | | if ( ! yyout ) | yyout = stdout; | | if ( ! YY_CURRENT_BUFFER ) { | yyensure_buffer_stack (); | YY_CURRENT_BUFFER_LVALUE = | yy_create_buffer(yyin,YY_BUF_SIZE ); | } | | yy_load_buffer_state( ); | } | | while ( 1 ) /* loops until end-of-file is reached */ | { | (yy_more_len) = 0; | if ( (yy_more_flag) ) | { | (yy_more_len) = (yy_c_buf_p) - (yytext_ptr); | (yy_more_flag) = 0; | } | yy_cp = (yy_c_buf_p); | | /* Support of yytext. */ | *yy_cp = (yy_hold_char); | | /* yy_bp points to the position in yy_ch_buf of the start of | * the current run. | */ | yy_bp = yy_cp; | | yy_current_state = (yy_start); | | (yy_state_ptr) = (yy_state_buf); | *(yy_state_ptr)++ = yy_current_state; | | yy_match: | do | { | register YY_CHAR yy_c = yy_ec[YY_SC_TO_UI(*yy_cp)]; | while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) | { | yy_current_state = (int) yy_def[yy_current_state]; | if ( yy_current_state >= 13 ) | yy_c = yy_meta[(unsigned int) yy_c]; | } | yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c]; | *(yy_state_ptr)++ = yy_current_state; | ++yy_cp; | } | while ( yy_base[yy_current_state] != 10 ); | | yy_find_action: | yy_current_state = *--(yy_state_ptr); | (yy_lp) = yy_accept[yy_current_state]; | find_rule: /* we branch to this label when backing up */ | for ( ; ; ) /* until we find what rule we matched */ | { | if ( (yy_lp) && (yy_lp) < yy_accept[yy_current_state + 1] ) | { | yy_act = yy_acclist[(yy_lp)]; | { | (yy_full_match) = yy_cp; | break; | } | } | --yy_cp; | yy_current_state = *--(yy_state_ptr); | (yy_lp) = yy_accept[yy_current_state]; | } | | YY_DO_BEFORE_ACTION; | | do_action: /* This label is used only to access EOF actions. */ | | switch ( yy_act ) | { /* beginning of action switch */ | case 1: | YY_RULE_SETUP | #line 2 "conftest.l" | { ECHO; } | YY_BREAK | case 2: | YY_RULE_SETUP | #line 3 "conftest.l" | { REJECT; } | YY_BREAK | case 3: | YY_RULE_SETUP | #line 4 "conftest.l" | { yymore (); } | YY_BREAK | case 4: | YY_RULE_SETUP | #line 5 "conftest.l" | { yyless (1); } | YY_BREAK | case 5: | YY_RULE_SETUP | #line 6 "conftest.l" | { /* IRIX 6.5 flex 2.5.4 underquotes its yyless argument. */ | yyless ((input () != 0)); } | YY_BREAK | case 6: | YY_RULE_SETUP | #line 8 "conftest.l" | { unput (yytext[0]); } | YY_BREAK | case 7: | YY_RULE_SETUP | #line 9 "conftest.l" | { BEGIN INITIAL; } | YY_BREAK | case 8: | YY_RULE_SETUP | #line 10 "conftest.l" | ECHO; | YY_BREAK | #line 805 "lex.yy.c" | case YY_STATE_EOF(INITIAL): | yyterminate(); | | case YY_END_OF_BUFFER: | { | /* Amount of text matched not including the EOB char. */ | int yy_amount_of_matched_text = (int) (yy_cp - (yytext_ptr)) - 1; | | /* Undo the effects of YY_DO_BEFORE_ACTION. */ | *yy_cp = (yy_hold_char); | YY_RESTORE_YY_MORE_OFFSET | | if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_NEW ) | { | /* We're scanning a new file or input source. It's | * possible that this happened because the user | * just pointed yyin at a new source and called | * yylex(). If so, then we have to assure | * consistency between YY_CURRENT_BUFFER and our | * globals. Here is the right place to do so, because | * this is the first action (other than possibly a | * back-up) that will match for the new input source. | */ | (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_n_chars; | YY_CURRENT_BUFFER_LVALUE->yy_input_file = yyin; | YY_CURRENT_BUFFER_LVALUE->yy_buffer_status = YY_BUFFER_NORMAL; | } | | /* Note that here we test for yy_c_buf_p "<=" to the position | * of the first EOB in the buffer, since yy_c_buf_p will | * already have been incremented past the NUL character | * (since all states make transitions on EOB to the | * end-of-buffer state). Contrast this with the test dh_auto_configure: ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libexecdir=${prefix}/lib/librostlab-blast --disable-maintainer-mode --disable-dependency-tracking --enable-doxygen-dot --enable-doxygen-pdf returned exit code 1 make[1]: *** [override_dh_auto_configure] Error 25 | * in input(). | */ | if ( (yy_c_buf_p) <= &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] ) | { /* This was really a NUL. */ | yy_state_type yy_next_state; | | (yy_c_buf_p) = (yytext_ptr) + yy_amount_of_matched_text; | | yy_current_state = yy_get_previous_state( ); | | /* Okay, we're now positioned to make the NUL | * transition. We couldn't have | * yy_get_previous_state() go ahead and do it | * for us because it doesn't know how to deal | * with the possibility of jamming (and we don't | * want to build jamming into it because then it | * will run more slowly). | */ | | yy_next_state = yy_try_NUL_trans( yy_current_state ); | | yy_bp = (yytext_ptr) + YY_MORE_ADJ; | | if ( yy_next_state ) | { | /* Consume the NUL. */ | yy_cp = ++(yy_c_buf_p); | yy_current_state = yy_next_state; | goto yy_match; | } | | else | { | yy_cp = (yy_c_buf_p); | goto yy_find_action; | } | } | | else switch ( yy_get_next_buffer( ) ) | { | case EOB_ACT_END_OF_FILE: | { | (yy_did_buffer_switch_on_eof) = 0; | | if ( yywrap( ) ) | { | /* Note: because we've taken care in | * yy_get_next_buffer() to have set up | * yytext, we can now set up | * yy_c_buf_p so that if some total | * hoser (like flex itself) wants to | * call the scanner after we return the | * YY_NULL, it'll still work - another | * YY_NULL will get returned. | */ | (yy_c_buf_p) = (yytext_ptr) + YY_MORE_ADJ; | | yy_act = YY_STATE_EOF(YY_START); | goto do_action; | } | | else | { | if ( ! (yy_did_buffer_switch_on_eof) ) | YY_NEW_FILE; | } | break; | } | | case EOB_ACT_CONTINUE_SCAN: | (yy_c_buf_p) = | (yytext_ptr) + yy_amount_of_matched_text; | | yy_current_state = yy_get_previous_state( ); | | yy_cp = (yy_c_buf_p); | yy_bp = (yytext_ptr) + YY_MORE_ADJ; | goto yy_match; | | case EOB_ACT_LAST_MATCH: | (yy_c_buf_p) = | &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)]; | | yy_current_state = yy_get_previous_state( ); | | yy_cp = (yy_c_buf_p); | yy_bp = (yytext_ptr) + YY_MORE_ADJ; | goto yy_find_action; | } | break; | } | | default: | YY_FATAL_ERROR( | "fatal flex scanner internal error--no action found" ); | } /* end of action switch */ | } /* end of scanning one token */ | } /* end of yylex */ | | /* yy_get_next_buffer - try to read in a new buffer | * | * Returns a code representing an action: | * EOB_ACT_LAST_MATCH - | * EOB_ACT_CONTINUE_SCAN - continue scanning from current position | * EOB_ACT_END_OF_FILE - end of file | */ | static int yy_get_next_buffer (void) | { | register char *dest = YY_CURRENT_BUFFER_LVALUE->yy_ch_buf; | register char *source = (yytext_ptr); | register int number_to_move, i; | int ret_val; | | if ( (yy_c_buf_p) > &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars) + 1] ) | YY_FATAL_ERROR( | "fatal flex scanner internal error--end of buffer missed" ); | | if ( YY_CURRENT_BUFFER_LVALUE->yy_fill_buffer == 0 ) | { /* Don't try to fill the buffer, so this is an EOF. */ | if ( (yy_c_buf_p) - (yytext_ptr) - YY_MORE_ADJ == 1 ) | { | /* We matched a single character, the EOB, so | * treat this as a final EOF. | */ | return EOB_ACT_END_OF_FILE; | } | | else | { | /* We matched some text prior to the EOB, first | * process it. | */ | return EOB_ACT_LAST_MATCH; | } | } | | /* Try to read more data. */ | | /* First move last chars to start of buffer. */ | number_to_move = (int) ((yy_c_buf_p) - (yytext_ptr)) - 1; | | for ( i = 0; i < number_to_move; ++i ) | *(dest++) = *(source++); | | if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_EOF_PENDING ) | /* don't do the read, it's not guaranteed to return an EOF, | * just force an EOF | */ | YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars) = 0; | | else | { | int num_to_read = | YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1; | | while ( num_to_read <= 0 ) | { /* Not enough room in the buffer - grow it. */ | | YY_FATAL_ERROR( | "input buffer overflow, can't enlarge buffer because scanner uses REJECT" ); | | } | | if ( num_to_read > YY_READ_BUF_SIZE ) | num_to_read = YY_READ_BUF_SIZE; | | /* Read in more data. */ | YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), | (yy_n_chars), (size_t) num_to_read ); | | YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); | } | | if ( (yy_n_chars) == 0 ) | { | if ( number_to_move == YY_MORE_ADJ ) | { | ret_val = EOB_ACT_END_OF_FILE; | yyrestart(yyin ); | } | | else | { | ret_val = EOB_ACT_LAST_MATCH; | YY_CURRENT_BUFFER_LVALUE->yy_buffer_status = | YY_BUFFER_EOF_PENDING; | } | } | | else | ret_val = EOB_ACT_CONTINUE_SCAN; | | if ((yy_size_t) ((yy_n_chars) + number_to_move) > YY_CURRENT_BUFFER_LVALUE->yy_buf_size) { | /* Extend the array by 50%, plus the number we really need. */ | yy_size_t new_size = (yy_n_chars) + number_to_move + ((yy_n_chars) >> 1); | YY_CURRENT_BUFFER_LVALUE->yy_ch_buf = (char *) yyrealloc((void *) YY_CURRENT_BUFFER_LVALUE->yy_ch_buf,new_size ); | if ( ! YY_CURRENT_BUFFER_LVALUE->yy_ch_buf ) | YY_FATAL_ERROR( "out of dynamic memory in yy_get_next_buffer()" ); | } | | (yy_n_chars) += number_to_move; | YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] = YY_END_OF_BUFFER_CHAR; | YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars) + 1] = YY_END_OF_BUFFER_CHAR; | | (yytext_ptr) = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[0]; | | return ret_val; | } | | /* yy_get_previous_state - get the state just before the EOB char was reached */ | | static yy_state_type yy_get_previous_state (void) | { | register yy_state_type yy_current_state; | register char *yy_cp; | | yy_current_state = (yy_start); | | (yy_state_ptr) = (yy_state_buf); | *(yy_state_ptr)++ = yy_current_state; | | for ( yy_cp = (yytext_ptr) + YY_MORE_ADJ; yy_cp < (yy_c_buf_p); ++yy_cp ) | { | register YY_CHAR yy_c = (*yy_cp ? yy_ec[YY_SC_TO_UI(*yy_cp)] : 1); | while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) | { | yy_current_state = (int) yy_def[yy_current_state]; | if ( yy_current_state >= 13 ) | yy_c = yy_meta[(unsigned int) yy_c]; | } | yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c]; | *(yy_state_ptr)++ = yy_current_state; | } | | return yy_current_state; | } | | /* yy_try_NUL_trans - try to make a transition on the NUL character | * | * synopsis | * next_state = yy_try_NUL_trans( current_state ); | */ | static yy_state_type yy_try_NUL_trans (yy_state_type yy_current_state ) | { | register int yy_is_jam; | | register YY_CHAR yy_c = 1; | while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) | { | yy_current_state = (int) yy_def[yy_current_state]; | if ( yy_current_state >= 13 ) | yy_c = yy_meta[(unsigned int) yy_c]; | } | yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c]; | yy_is_jam = (yy_current_state == 12); | if ( ! yy_is_jam ) | *(yy_state_ptr)++ = yy_current_state; | | return yy_is_jam ? 0 : yy_current_state; | } | | static void yyunput (int c, register char * yy_bp ) | { | register char *yy_cp; | | yy_cp = (yy_c_buf_p); | | /* undo effects of setting up yytext */ | *yy_cp = (yy_hold_char); | | if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 ) | { /* need to shift things up to make room */ | /* +2 for EOB chars. */ | register int number_to_move = (yy_n_chars) + 2; | register char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[ | YY_CURRENT_BUFFER_LVALUE->yy_buf_size + 2]; | register char *source = | &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]; | | while ( source > YY_CURRENT_BUFFER_LVALUE->yy_ch_buf ) | *--dest = *--source; | | yy_cp += (int) (dest - source); | yy_bp += (int) (dest - source); | YY_CURRENT_BUFFER_LVALUE->yy_n_chars = | (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_buf_size; | | if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 ) | YY_FATAL_ERROR( "flex scanner push-back overflow" ); | } | | *--yy_cp = (char) c; | | (yytext_ptr) = yy_bp; | (yy_hold_char) = *yy_cp; | (yy_c_buf_p) = yy_cp; | } | | #ifndef YY_NO_INPUT | #ifdef __cplusplus | static int yyinput (void) | #else | static int input (void) | #endif | | { | int c; | | *(yy_c_buf_p) = (yy_hold_char); | | if ( *(yy_c_buf_p) == YY_END_OF_BUFFER_CHAR ) | { | /* yy_c_buf_p now points to the character we want to return. | * If this occurs *before* the EOB characters, then it's a | * valid NUL; if not, then we've hit the end of the buffer. | */ | if ( (yy_c_buf_p) < &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] ) | /* This was really a NUL. */ | *(yy_c_buf_p) = '\0'; | | else | { /* need more input */ | int offset = (yy_c_buf_p) - (yytext_ptr); | ++(yy_c_buf_p); | | switch ( yy_get_next_buffer( ) ) | { | case EOB_ACT_LAST_MATCH: | /* This happens because yy_g_n_b() make: | * sees that we've accumulated a *** [build-arch] Error 2 | * token and flags that we need to | * try matching the token before | * proceeding. But for input(), | * there's no matching to consider. | * So convert the EOB_ACT_LAST_MATCH | * to EOB_ACT_END_OF_FILE. | */ | | /* Reset buffer status. */ | yyrestart(yyin ); | | /*FALLTHROUGH*/ | | case EOB_ACT_END_OF_FILE: | { | if ( yywrap( ) ) | return EOF; | | if ( ! (yy_did_buffer_switch_on_eof) ) | YY_NEW_FILE; | #ifdef __cplusplus | return yyinput(); | #else | return input(); | #endif | } | | case EOB_ACT_CONTINUE_SCAN: | (yy_c_buf_p) = (yytext_ptr) + offset; | break; | } | } | } | | c = *(unsigned char *) (yy_c_buf_p); /* cast for 8-bit char's */ | *(yy_c_buf_p) = '\0'; /* preserve yytext */ | (yy_hold_char) = *++(yy_c_buf_p); | | return c; | } | #endif /* ifndef YY_NO_INPUT */ | | /** Immediately switch to a different input stream. | * @param input_file A readable stream. | * | * @note This function does not reset the start condition to @c INITIAL . | */ | void yyrestart (FILE * input_file ) | { | | if ( ! YY_CURRENT_BUFFER ){ | yyensure_buffer_stack (); | YY_CURRENT_BUFFER_LVALUE = | yy_create_buffer(yyin,YY_BUF_SIZE ); | } | | yy_init_buffer(YY_CURRENT_BUFFER,input_file ); | yy_load_buffer_state( ); | } | | /** Switch to a different input buffer. | * @param new_buffer The new input buffer. | * | */ | void yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ) | { | | /* TODO. We should be able to replace this entire function body | * with | * yypop_buffer_state(); dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 | * yypush_buffer_state(new_buffer); | */ | yyensure_buffer_stack (); | if ( YY_CURRENT_BUFFER == new_buffer ) | return; | | if ( YY_CURRENT_BUFFER ) | { | /* Flush out information for old buffer. */ | *(yy_c_buf_p) = (yy_hold_char); | YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = (yy_c_buf_p); | YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); | } | | YY_CURRENT_BUFFER_LVALUE = new_buffer; | yy_load_buffer_state( ); | | /* We don't actually know whether we did this switch during | * EOF (yywrap()) processing, but the only time this flag | * is looked at is after yywrap() is called, so it's safe | * to go ahead and always set it. | */ | (yy_did_buffer_switch_on_eof) = 1; | } | | static void yy_load_buffer_state (void) | { | (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_n_chars; | (yytext_ptr) = (yy_c_buf_p) = YY_CURRENT_BUFFER_LVALUE->yy_buf_pos; | yyin = YY_CURRENT_BUFFER_LVALUE->yy_input_file; | (yy_hold_char) = *(yy_c_buf_p); | } | | /** Allocate and initialize an input buffer state. | * @param file A readable stream. | * @param size The character buffer size in bytes. When in doubt, use @c YY_BUF_SIZE. | * | * @return the allocated buffer state. | */ | YY_BUFFER_STATE yy_create_buffer (FILE * file, int size ) | { | YY_BUFFER_STATE b; | | b = (YY_BUFFER_STATE) yyalloc(sizeof( struct yy_buffer_state ) ); | if ( ! b ) | YY_FATAL_ERROR( "out of dynamic memory in yy_create_buffer()" ); | | b->yy_buf_size = size; | | /* yy_ch_buf has to be 2 characters longer than the size given because | * we need to put in 2 end-of-buffer characters. | */ | b->yy_ch_buf = (char *) yyalloc(b->yy_buf_size + 2 ); | if ( ! b->yy_ch_buf ) | YY_FATAL_ERROR( "out of dynamic memory in yy_create_buffer()" ); | | b->yy_is_our_buffer = 1; | | yy_init_buffer(b,file ); | | return b; | } | | /** Destroy the buffer. | * @param b a buffer created with yy_create_buffer() | * | */ | void yy_delete_buffer (YY_BUFFER_STATE b ) | { | | if ( ! b ) | return; | | if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */ | YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0; | | if ( b->yy_is_our_buffer ) | yyfree((void *) b->yy_ch_buf ); | | yyfree((void *) b ); | } | | #ifndef __cplusplus | extern int isatty (int ); | #endif /* __cplusplus */ | | /* Initializes or reinitializes a buffer. | * This function is sometimes called more than once on the same buffer, | * such as during a yyrestart() or at EOF. | */ | static void yy_init_buffer (YY_BUFFER_STATE b, FILE * file ) | | { | int oerrno = errno; | | yy_flush_buffer(b ); | | b->yy_input_file = file; | b->yy_fill_buffer = 1; | | /* If b is the current buffer, then yy_init_buffer was _probably_ | * called from yyrestart() or through yy_get_next_buffer. | * In that case, we don't want to reset the lineno or column. | */ | if (b != YY_CURRENT_BUFFER){ | b->yy_bs_lineno = 1; | b->yy_bs_column = 0; | } | | b->yy_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0; | | errno = oerrno; | } | | /** Discard all buffered characters. On the next scan, YY_INPUT will be called. | * @param b the buffer state to be flushed, usually @c YY_CURRENT_BUFFER. | * | */ | void yy_flush_buffer (YY_BUFFER_STATE b ) | { | if ( ! b ) | return; | | b->yy_n_chars = 0; | | /* We always need two end-of-buffer characters. The first causes | * a transition to the end-of-buffer state. The second causes | * a jam in that state. | */ | b->yy_ch_buf[0] = YY_END_OF_BUFFER_CHAR; | b->yy_ch_buf[1] = YY_END_OF_BUFFER_CHAR; | | b->yy_buf_pos = &b->yy_ch_buf[0]; | | b->yy_at_bol = 1; | b->yy_buffer_status = YY_BUFFER_NEW; | | if ( b == YY_CURRENT_BUFFER ) | yy_load_buffer_state( ); | } | | /** Pushes the new state onto the stack. The new state becomes | * the current state. This function will allocate the stack | * if necessary. | * @param new_buffer The new state. | * | */ | void yypush_buffer_state (YY_BUFFER_STATE new_buffer ) | { | if (new_buffer == NULL) | return; | | yyensure_buffer_stack(); | | /* This block is copied from yy_switch_to_buffer. */ | if ( YY_CURRENT_BUFFER ) | { | /* Flush out information for old buffer. */ | *(yy_c_buf_p) = (yy_hold_char); | YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = (yy_c_buf_p); | YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); | } | | /* Only push if top exists. Otherwise, replace top. */ | if (YY_CURRENT_BUFFER) | (yy_buffer_stack_top)++; | YY_CURRENT_BUFFER_LVALUE = new_buffer; | | /* copied from yy_switch_to_buffer. */ | yy_load_buffer_state( ); | (yy_did_buffer_switch_on_eof) = 1; | } | | /** Removes and deletes the top of the stack, if present. | * The next element becomes the new top. | * | */ | void yypop_buffer_state (void) | { | if (!YY_CURRENT_BUFFER) | return; | | yy_delete_buffer(YY_CURRENT_BUFFER ); | YY_CURRENT_BUFFER_LVALUE = NULL; | if ((yy_buffer_stack_top) > 0) | --(yy_buffer_stack_top); | | if (YY_CURRENT_BUFFER) { | yy_load_buffer_state( ); | (yy_did_buffer_switch_on_eof) = 1; | } | } | | /* Allocates the stack if it does not exist. | * Guarantees space for at least one push. | */ | static void yyensure_buffer_stack (void) | { | int num_to_alloc; | | if (!(yy_buffer_stack)) { | | /* First allocation is just for 2 elements, since we don't know if this | * scanner will even need a stack. We use 2 instead of 1 to avoid an | * immediate realloc on the next call. | */ | num_to_alloc = 1; | (yy_buffer_stack) = (struct yy_buffer_state**)yyalloc | (num_to_alloc * sizeof(struct yy_buffer_state*) | ); | if ( ! (yy_buffer_stack) ) | YY_FATAL_ERROR( "out of dynamic memory in yyensure_buffer_stack()" ); | | memset((yy_buffer_stack), 0, num_to_alloc * sizeof(struct yy_buffer_state*)); | | (yy_buffer_stack_max) = num_to_alloc; | (yy_buffer_stack_top) = 0; | return; | } | | if ((yy_buffer_stack_top) >= ((yy_buffer_stack_max)) - 1){ | | /* Increase the buffer to prepare for a possible push. */ | int grow_size = 8 /* arbitrary grow size */; | | num_to_alloc = (yy_buffer_stack_max) + grow_size; | (yy_buffer_stack) = (struct yy_buffer_state**)yyrealloc | ((yy_buffer_stack), | num_to_alloc * sizeof(struct yy_buffer_state*) | ); | if ( ! (yy_buffer_stack) ) | YY_FATAL_ERROR( "out of dynamic memory in yyensure_buffer_stack()" ); | | /* zero only the new slots.*/ | memset((yy_buffer_stack) + (yy_buffer_stack_max), 0, grow_size * sizeof(struct yy_buffer_state*)); | (yy_buffer_stack_max) = num_to_alloc; | } | } | | /** Setup the input buffer state to scan directly from a user-specified character buffer. | * @param base the character buffer | * @param size the size in bytes of the character buffer | * | * @return the newly allocated buffer state object. | */ | YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size ) | { | YY_BUFFER_STATE b; | | if ( size < 2 || | base[size-2] != YY_END_OF_BUFFER_CHAR || | base[size-1] != YY_END_OF_BUFFER_CHAR ) | /* They forgot to leave room for the EOB's. */ | return 0; | | b = (YY_BUFFER_STATE) yyalloc(sizeof( struct yy_buffer_state ) ); | if ( ! b ) | YY_FATAL_ERROR( "out of dynamic memory in yy_scan_buffer()" ); | | b->yy_buf_size = size - 2; /* "- 2" to take care of EOB's */ | b->yy_buf_pos = b->yy_ch_buf = base; | b->yy_is_our_buffer = 0; | b->yy_input_file = 0; | b->yy_n_chars = b->yy_buf_size; | b->yy_is_interactive = 0; | b->yy_at_bol = 1; | b->yy_fill_buffer = 0; | b->yy_buffer_status = YY_BUFFER_NEW; | | yy_switch_to_buffer(b ); | | return b; | } | | /** Setup the input buffer state to scan a string. The next call to yylex() will | * scan from a @e copy of @a str. | * @param yystr a NUL-terminated string to scan | * | * @return the newly allocated buffer state object. | * @note If you want to scan bytes that may contain NUL values, then use | * yy_scan_bytes() instead. | */ | YY_BUFFER_STATE yy_scan_string (yyconst char * yystr ) | { | | return yy_scan_bytes(yystr,strlen(yystr) ); | } | | /** Setup the input buffer state to scan the given bytes. The next call to yylex() will | * scan from a @e copy of @a bytes. | * @param yybytes the byte buffer to scan | * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes. | * | * @return the newly allocated buffer state object. | */ | YY_BUFFER_STATE yy_scan_bytes (yyconst char * yybytes, int _yybytes_len ) | { | YY_BUFFER_STATE b; | char *buf; | yy_size_t n; | int i; | | /* Get memory for full buffer, including space for trailing EOB's. */ | n = _yybytes_len + 2; | buf = (char *) yyalloc(n ); | if ( ! buf ) | YY_FATAL_ERROR( "out of dynamic memory in yy_scan_bytes()" ); | | for ( i = 0; i < _yybytes_len; ++i ) | buf[i] = yybytes[i]; | | buf[_yybytes_len] = buf[_yybytes_len+1] = YY_END_OF_BUFFER_CHAR; | | b = yy_scan_buffer(buf,n ); | if ( ! b ) | YY_FATAL_ERROR( "bad buffer in yy_scan_bytes()" ); | | /* It's okay to grow etc. this buffer, and we should throw it | * away when we're done. | */ | b->yy_is_our_buffer = 1; | | return b; | } | | #ifndef YY_EXIT_FAILURE | #define YY_EXIT_FAILURE 2 | #endif | | static void yy_fatal_error (yyconst char* msg ) | { | (void) fprintf( stderr, "%s\n", msg ); | exit( YY_EXIT_FAILURE ); | } | | /* Redefine yyless() so it works in section 3 code. */ | | #undef yyless | #define yyless(n) \ | do \ | { \ | /* Undo effects of setting up yytext. */ \ | int yyless_macro_arg = (n); \ | YY_LESS_LINENO(yyless_macro_arg);\ | yytext[yyleng] = (yy_hold_char); \ | (yy_c_buf_p) = yytext + yyless_macro_arg; \ | (yy_hold_char) = *(yy_c_buf_p); \ | *(yy_c_buf_p) = '\0'; \ | yyleng = yyless_macro_arg; \ | } \ | while ( 0 ) | | /* Accessor methods (get/set functions) to struct members. */ | | /** Get the current line number. | * | */ | int yyget_lineno (void) | { | | return yylineno; | } | | /** Get the input stream. | * | */ | FILE *yyget_in (void) | { | return yyin; | } | | /** Get the output stream. | * | */ | FILE *yyget_out (void) | { | return yyout; | } | | /** Get the length of the current token. | * | */ | int yyget_leng (void) | { | return yyleng; | } | | /** Get the current token. | * | */ | | char *yyget_text (void) | { | return yytext; | } | | /** Set the current line number. | * @param line_number | * | */ | void yyset_lineno (int line_number ) | { | | yylineno = line_number; | } | | /** Set the input stream. This does not discard the current | * input buffer. | * @param in_str A readable stream. | * | * @see yy_switch_to_buffer | */ | void yyset_in (FILE * in_str ) | { | yyin = in_str ; | } | | void yyset_out (FILE * out_str ) | { | yyout = out_str ; | } | | int yyget_debug (void) | { | return yy_flex_debug; | } | | void yyset_debug (int bdebug ) | { | yy_flex_debug = bdebug ; | } | | static int yy_init_globals (void) | { | /* Initialization is the same as for the non-reentrant scanner. | * This function is called from yylex_destroy(), so don't allocate here. | */ | | (yy_buffer_stack) = 0; | (yy_buffer_stack_top) = 0; | (yy_buffer_stack_max) = 0; | (yy_c_buf_p) = (char *) 0; | (yy_init) = 0; | (yy_start) = 0; | | (yy_state_buf) = 0; | (yy_state_ptr) = 0; | (yy_full_match) = 0; | (yy_lp) = 0; | | /* Defined in main.c */ | #ifdef YY_STDINIT | yyin = stdin; | yyout = stdout; | #else | yyin = (FILE *) 0; | yyout = (FILE *) 0; | #endif | | /* For future reference: Set errno on error, since we are called by | * yylex_init() | */ | return 0; | } | | /* yylex_destroy is for both reentrant and non-reentrant scanners. */ | int yylex_destroy (void) | { | | /* Pop the buffer stack, destroying each element. */ | while(YY_CURRENT_BUFFER){ | yy_delete_buffer(YY_CURRENT_BUFFER ); | YY_CURRENT_BUFFER_LVALUE = NULL; | yypop_buffer_state(); | } | | /* Destroy the stack itself. */ | yyfree((yy_buffer_stack) ); | (yy_buffer_stack) = NULL; | | yyfree ( (yy_state_buf) ); | (yy_state_buf) = NULL; | | /* Reset the globals. This is important in a non-reentrant scanner so the next time | * yylex() is called, initialization will occur. */ | yy_init_globals( ); | | return 0; | } | | /* | * Internal utility routines. | */ | | #ifndef yytext_ptr | static void yy_flex_strncpy (char* s1, yyconst char * s2, int n ) | { | register int i; | for ( i = 0; i < n; ++i ) | s1[i] = s2[i]; | } | #endif | | #ifdef YY_NEED_STRLEN | static int yy_flex_strlen (yyconst char * s ) | { | register int n; | for ( n = 0; s[n]; ++n ) | ; | | return n; | } | #endif | | void *yyalloc (yy_size_t size ) | { | return (void *) malloc( size ); | } | | void *yyrealloc (void * ptr, yy_size_t size ) | { | /* The cast to (char *) in the following accommodates both | * implementations that use char* generic pointers, and those | * that use void* generic pointers. It works with the latter | * because both ANSI C and C++ allow castless assignment from | * any pointer type to void*, and deal with argument conversions | * as though doing an assignment. | */ | return (void *) realloc( (char *) ptr, size ); | } | | void yyfree (void * ptr ) | { | free( (char *) ptr ); /* see yyrealloc() for (char *) cast */ | } | | #define YYTABLES_NAME "yytables" | | #line 10 "conftest.l" | | | #ifdef YYTEXT_POINTER | extern char *yytext; | #endif | int | main (void) | { | return ! yylex () + ! yywrap (); | } configure:15235: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c -lfl >&5 configure:15235: $? = 0 configure:15245: result: -lfl configure:15251: checking whether yytext is a pointer configure:15268: gcc -o conftest -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro conftest.c -lfl >&5 configure:15268: $? = 0 configure:15276: result: yes configure:15296: checking rostlab/aux_functions.h usability configure:15296: g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 conftest.cpp >&5 In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:36:1: error: unknown type name '__extern_always_inline' __fortify_function __wur char * ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:36:20: error: expected unqualified-id __fortify_function __wur char * ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:297:17: note: expanded from macro '__wur' # define __wur __attribute_warn_unused_result__ ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:295:4: note: expanded from macro '__attribute_warn_unused_result__' __attribute__ ((__warn_unused_result__)) ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:63:1: error: unknown type name '__extern_always_inline' __fortify_function int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:63:20: error: expected unqualified-id __fortify_function int ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:82:1: error: unknown type name '__extern_always_inline' __fortify_function __wur int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:82:20: error: expected unqualified-id __fortify_function __wur int ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:297:17: note: expanded from macro '__wur' # define __wur __attribute_warn_unused_result__ ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:295:4: note: expanded from macro '__attribute_warn_unused_result__' __attribute__ ((__warn_unused_result__)) ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:1: error: unknown type name '__extern_always_inline' __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:26: error: expected ';' after top level declarator __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:133:8: error: reference to 'size_t' is ambiguous extern size_t __REDIRECT_NTH (__wcstombs_alias, ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:136:11: error: reference to 'size_t' is ambiguous size_t __len), wcstombs); ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:137:8: error: reference to 'size_t' is ambiguous extern size_t __REDIRECT_NTH (__wcstombs_chk_warn, ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:140:11: error: reference to 'size_t' is ambiguous size_t __len, size_t __dstlen), __wcstombs_chk) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:140:25: error: reference to 'size_t' is ambiguous size_t __len, size_t __dstlen), __wcstombs_chk) ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:190:11: note: expanded from macro '__REDIRECT_NTH' name proto __THROW __asm__ (__ASMNAME (#alias)) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:112:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:1: error: unknown type name '__extern_always_inline' __fortify_function size_t ^ /usr/include/x86_64-linux-gnu/sys/cdefs.h:143:28: note: expanded from macro '__fortify_function' #define __fortify_function __extern_always_inline __attribute_artificial__ ^ In file included from conftest.cpp:32: In file included from /usr/include/stdlib.h:957: /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:26: error: expected ';' after top level declarator __fortify_function size_t ^ In file included from conftest.cpp:43: /usr/include/string.h:43:8: error: reference to 'size_t' is ambiguous size_t __n) __THROW __nonnull ((1, 2)); ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:43: /usr/include/string.h:46:56: error: reference to 'size_t' is ambiguous extern void *memmove (void *__dest, const void *__src, size_t __n) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:43: /usr/include/string.h:55:18: error: reference to 'size_t' is ambiguous int __c, size_t __n) ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ In file included from conftest.cpp:43: /usr/include/string.h:62:42: error: reference to 'size_t' is ambiguous extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ /usr/include/x86_64-linux-gnu/bits/stdlib.h:143:20: note: candidate found by name lookup is 'size_t' __fortify_function size_t ^ /usr/include/clang/3.2/include/stddef.h:35:33: note: candidate found by name lookup is 'size_t' typedef __typeof__(sizeof(int)) size_t; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. configure:15296: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "librostlab-blast" | #define PACKAGE_TARNAME "librostlab-blast" | #define PACKAGE_VERSION "1.0.1" | #define PACKAGE_STRING "librostlab-blast 1.0.1" | #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" | #define PACKAGE_URL "" | #define PACKAGE "librostlab-blast" | #define VERSION "1.0.1" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define YYTEXT_POINTER 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | #include configure:15296: result: no configure:15296: checking rostlab/aux_functions.h presence configure:15296: g++ -E -D_FORTIFY_SOURCE=2 conftest.cpp configure:15296: $? = 0 configure:15296: result: yes configure:15296: WARNING: rostlab/aux_functions.h: present but cannot be compiled configure:15296: WARNING: rostlab/aux_functions.h: check for missing prerequisite headers? configure:15296: WARNING: rostlab/aux_functions.h: see the Autoconf documentation configure:15296: WARNING: rostlab/aux_functions.h: section "Present But Cannot Be Compiled" configure:15296: WARNING: rostlab/aux_functions.h: proceeding with the compiler's result configure:15296: checking for rostlab/aux_functions.h configure:15296: result: no ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-pc-linux-gnu ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set=set ac_cv_env_CFLAGS_value='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value=-D_FORTIFY_SOURCE=2 ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set=set ac_cv_env_CXXFLAGS_value='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_DOXYGEN_PAPER_SIZE_set= ac_cv_env_DOXYGEN_PAPER_SIZE_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value=-Wl,-z,relro ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_YACC_set= ac_cv_env_YACC_value= ac_cv_env_YFLAGS_set= ac_cv_env_YFLAGS_value= ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=x86_64-linux-gnu ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_header_dlfcn_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_memory_h=yes ac_cv_header_rostlab_aux_functions_h=no ac_cv_header_stdc=yes ac_cv_header_stdint_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_host=x86_64-pc-linux-gnu ac_cv_lib_lex=-lfl ac_cv_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_FGREP='/bin/grep -F' ac_cv_path_GREP=/bin/grep ac_cv_path_SED=/bin/sed ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AWK=mawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_CXXCPP='g++ -E' ac_cv_prog_LEX=flex ac_cv_prog_YACC='bison -y' ac_cv_prog_ac_ct_AR=ar ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_ac_ct_OBJDUMP=objdump ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_ac_ct_STRIP=strip ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ac_cv_prog_lex_root=lex.yy ac_cv_prog_lex_yytext_pointer=yes ac_cv_prog_make_make_set=yes am_cv_CC_dependencies_compiler_type=none am_cv_CXX_dependencies_compiler_type=none lt_cv_ar_at_file=@ lt_cv_archive_cmds_need_lc=no lt_cv_deplibs_check_method=pass_all lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_ld_reload_flag=-r lt_cv_nm_interface='BSD nm' lt_cv_objdir=.libs lt_cv_path_LD=/usr/bin/ld lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64' lt_cv_path_NM='/usr/bin/nm -B' lt_cv_path_mainfest_tool=no lt_cv_prog_compiler_c_o=yes lt_cv_prog_compiler_c_o_CXX=yes lt_cv_prog_compiler_pic='-fPIC -DPIC' lt_cv_prog_compiler_pic_CXX='-fPIC -DPIC' lt_cv_prog_compiler_pic_works=yes lt_cv_prog_compiler_pic_works_CXX=yes lt_cv_prog_compiler_rtti_exceptions=yes lt_cv_prog_compiler_static_works=yes lt_cv_prog_compiler_static_works_CXX=yes lt_cv_prog_gnu_ld=yes lt_cv_prog_gnu_ldcxx=yes lt_cv_sharedlib_from_linklib_cmd='printf %s\n' lt_cv_shlibpath_overrides_runpath=no lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\''' lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_max_cmd_len=3458764513820540925 lt_cv_to_host_file_cmd=func_convert_file_noop lt_cv_to_tool_file_cmd=func_convert_file_noop ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /«PKGBUILDDIR»/missing --run aclocal-1.11' AMDEPBACKSLASH='' AMDEP_FALSE='' AMDEP_TRUE='#' AMTAR='$${TAR-tar}' AR='ar' AUTOCONF='${SHELL} /«PKGBUILDDIR»/missing --run autoconf' AUTOHEADER='${SHELL} /«PKGBUILDDIR»/missing --run autoheader' AUTOMAKE='${SHELL} /«PKGBUILDDIR»/missing --run automake-1.11' AWK='mawk' CC='gcc' CCDEPMODE='depmode=none' CFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' CPP='gcc -E' CPPFLAGS='-D_FORTIFY_SOURCE=2' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=none' CXXFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' DLLTOOL='false' DOXYGEN_PAPER_SIZE='' DSYMUTIL='' DUMPBIN='' DX_COND_chi_FALSE='' DX_COND_chi_TRUE='' DX_COND_chm_FALSE='' DX_COND_chm_TRUE='' DX_COND_doc_FALSE='' DX_COND_doc_TRUE='' DX_COND_dot_FALSE='' DX_COND_dot_TRUE='' DX_COND_html_FALSE='' DX_COND_html_TRUE='' DX_COND_latex_FALSE='' DX_COND_latex_TRUE='' DX_COND_man_FALSE='' DX_COND_man_TRUE='' DX_COND_pdf_FALSE='' DX_COND_pdf_TRUE='' DX_COND_ps_FALSE='' DX_COND_ps_TRUE='' DX_COND_rtf_FALSE='' DX_COND_rtf_TRUE='' DX_COND_xml_FALSE='' DX_COND_xml_TRUE='' DX_CONFIG='' DX_DOCDIR='' DX_DOT='' DX_DOXYGEN='' DX_DVIPS='' DX_EGREP='' DX_ENV='' DX_FLAG_chi='' DX_FLAG_chm='' DX_FLAG_doc='' DX_FLAG_dot='' DX_FLAG_html='' DX_FLAG_man='' DX_FLAG_pdf='' DX_FLAG_ps='' DX_FLAG_rtf='' DX_FLAG_xml='' DX_HHC='' DX_LATEX='' DX_MAKEINDEX='' DX_PDFLATEX='' DX_PERL='' DX_PROJECT='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' FGREP='/bin/grep -F' GREP='/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LD='/usr/bin/ld -m elf_x86_64' LDFLAGS='-Wl,-z,relro' LEX='flex' LEXLIB='-lfl' LEX_OUTPUT_ROOT='lex.yy' LIBOBJS='' LIBS='' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /«PKGBUILDDIR»/missing --run makeinfo' MANIFEST_TOOL=':' MKDIR_P='/bin/mkdir -p' NM='/usr/bin/nm -B' NMEDIT='' OBJDUMP='objdump' OBJEXT='o' OTOOL64='' OTOOL='' PACKAGE='librostlab-blast' PACKAGE_BUGREPORT='https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast' PACKAGE_NAME='librostlab-blast' PACKAGE_STRING='librostlab-blast 1.0.1' PACKAGE_TARNAME='librostlab-blast' PACKAGE_URL='' PACKAGE_VERSION='1.0.1' PATH_SEPARATOR=':' RANLIB='ranlib' SED='/bin/sed' SET_MAKE='' SHELL='/bin/bash' STRIP='strip' VERSION='1.0.1' YACC='bison -y' YFLAGS='' ac_ct_AR='ar' ac_ct_CC='gcc' ac_ct_CXX='g++' ac_ct_DUMPBIN='' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='' am__fastdepCC_FALSE='' am__fastdepCC_TRUE='#' am__fastdepCXX_FALSE='' am__fastdepCXX_TRUE='#' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='x86_64-pc-linux-gnu' build_alias='x86_64-linux-gnu' build_cpu='x86_64' build_os='linux-gnu' build_vendor='pc' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='x86_64-pc-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='pc' htmldir='${docdir}' includedir='${prefix}/include' infodir='${prefix}/share/info' install_sh='${SHELL} /«PKGBUILDDIR»/install-sh' libdir='${exec_prefix}/lib' libexecdir='${prefix}/lib/librostlab-blast' localedir='${datarootdir}/locale' localstatedir='/var' mandir='${prefix}/share/man' mkdir_p='/bin/mkdir -p' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/usr' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "librostlab-blast" #define PACKAGE_TARNAME "librostlab-blast" #define PACKAGE_VERSION "1.0.1" #define PACKAGE_STRING "librostlab-blast 1.0.1" #define PACKAGE_BUGREPORT "https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab-blast" #define PACKAGE_URL "" #define PACKAGE "librostlab-blast" #define VERSION "1.0.1" #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_DLFCN_H 1 #define LT_OBJDIR ".libs/" #define YYTEXT_POINTER 1 configure: exit 1 make[1]: Leaving directory `/«PKGBUILDDIR»' ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130128-0439 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 1860 Build-Time: 9 Distribution: unstable Fail-Stage: build Install-Time: 33 Job: librostlab-blast_1.0.1-2 Package: librostlab-blast Package-Time: 70 Source-Version: 1.0.1-2 Space: 1860 Status: attempted Version: 1.0.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130128-0439 Build needed 00:01:10, 1860k disc space DC-Status: Failed 70.695458s DC-Time-Estimation: 70.695458 versus expected 268 (r/m: 2.7909083211541 ; m: 70.695458)